########################################################################### # Things to do # # (1) database extract programs to write to a local directory # (2) test local directory as well as local files (see above) # (3) make list of missing data files # (4) update web page examples to match the tests # (5) tests for @list and other odd USA types # ########################################################################### # This is the qatest.dat file that is used by scripts/qatest.pl # # The script should be run from the directory test/qa # # Additional input data is expected to be found in the directory test/data # # If no argument is given to the script it will run through all of the # entries in this file. If an argument is supplied it will search for # the entry whose ID name matches the argument and will run that one. # # To run the script and retain the files created during the test, use # ../../scripts/qatest.pl -kk # # The results of the QA tests will be stored in the file # test/qa/qatest.log # # Typical example entry for an EMBOSS package program (AP line) # See below for AA/AB (EMBASSY) and AQ (make check) entries # # ID programname-ex (the ID name of this test) # UC text (not used in the QA test - used in the HTML documentation) # AP programname (the name of the application to test) # CL (the command-line arguments to use after the application name) # IN (a response to a prompt for input using the default) # IN text (a response to a prompt using a non-default input) # IK text (input keystrokes, not responses to prompts) # FI filename (an expected output filename) # FZ integer (the expected size in bytes of the above filename) # FC integer (the expected number of lines in the above file) # FP /regexp/ (an expected perl regular expression in the above file) # FP integer /regexp/ (a regexp that is expected integer number of times) # FI stderr (these are standard checks on the expected error reports) # FC = 2 # FP 0 /Warning: / # FP 0 /Error: / # FP 0 /Died: / # // (marks the end of the entry) # # ID identifier # The identifier is formed from the name of the application being # tested and a tag to indicate what sort of test is being performed. # The identifier is used to create a directory test/qa/. # Typical tags are: # -ex = example used to create the HTML documentation # -ex2, -ex3 = further examples used in the documentation # In general, all documentation examples should have tests # to check the documentation is correct. # -keep If the test has a "DL keep" line the resulting files are kept. # Used for database indexing - later tests will use the results! # -fail Testing a failure condition (ER line) # AA Application name for an EMBASSY package application. # This is used for the command line and for reporting statistics. # The application must be built by "make" for the EMBASSY package # defined in the AB line for this test definition. # If the application is not found, qatest can assume this # EMBASSY package was not installed. # AB EMBASSY package name # Used to inform the qatest script that a test depends on # installation of an EMBASSY package and may fail to find the binary. # AP Application name for EMBOSS application # This is used for the command line and for reporting statistics. # The application must be a standard EMBOSS application, built by make. # The test must succeed. # AQ Application name for "make check" application # This is used for the command line and for reporting statistics. # The application must be built by "make check". # The qatest script will look in the build directory as this # application will not be installed. # If the application is not found, qatest can assume "make # check" was not run. # CC Comment # Used in commenting on failed tests # This comment will appear in the test output on failure as a guide # to an acceptable failure condition (check the error message too!) # See ## lines for general comments within the definition # CL Command line # (Optional) # This is the rest of the command line. # Multiple CL lines are appended with a space in between. # DI Directory # Name of a directory created in the results directory # No tests currently for the contents, but a QQ postprocessing # command could be used to list the contents to another file. # DL 'success' or 'all' or 'keep' # (Optional) # 'success' = delete the test directory on success (the default) # 'all' = delete the test directory always # 'keep' = keep the test results directory always # (used if another test reuses the results, # e.g. database indexing) # ER error return code # (Optional) # Error code expecte. # Used for tests that are test failure conditions. # The test reports an error if the error code is not found # FC [<=>] number # = nn Number of lines # > nn More than nn lines # < nn Less than nn lines # FI File name # (Required for all output files created) # stdout and stderr are assumed to exist and be empty unless stated. # FP File pattern # (Required for all non stdout and stderr files) # perl /regexp/ to be found in the preceeding 'FI' file. # The /regexp/ may be preceded by an optional count to check exact # number. # As an extra check, stderr (which often contains the user prompts) # should be checked for absence of warning, error and died messages. # FZ [<=>] number # (Required for all non stdout and stderr files) # File size test on the preceeding 'FI' file. # The file size may be qualified with an optional relation '=', '>' etc. # Implicit test for zero size stdout/stderr unless stated. # IC text # (Optional) # This information is not used in the QA testing. # It is used by scripts/makeexample.pl when creating the HTML # documentation files to annotate the input. # IN Line input # (Required for each prompted input) # If there is nothing on the line, then an empty line is input to the # application. (Obvious really, but needs to be said) # Care is needed if standard options are added/removed from the program. # OC text # (Optional) # This information is not used in the QA testing. # It is used by scripts/makeexample.pl when creating the HTML # documentation files to annotate the output. # PP Preprocessor command # (Optional) # Command executed (by /bin/sh) before the test. # Each PP line is a separate command. Long lines are not concatenated. # e.g. Set an environment variable required by the application. # The variable should always be exported (this is /bin/sh), for example: # PP EMBOSS_ACDROOT=../../acd # PP export EMBOSS_ACDROOT # QQ Postprocessor command # (Optional) # Command executed (by /bin/sh) after the test. # Each QQ line is a separate command. Long lines are not concatenated. # Not used at present. Most likely application is to list the # contents of a directory to another file, which can then be # tested for size and patterns. # RQ required # Required external programs. For example, srs for tests that # use getz, or clustalw for emma # TI seconds # Timeout for test. The default is 60 seconds. Some examples # can take longer on a heavily loaded system. # UC text # (Optional) # This information is not used in the QA testing. # It is used by scripts/makeexample.pl when creating the HTML # documentation files to annotate the examples of usage. # ## Comment # (Optional) # This is a comment. # Double # is required. # This is only a comment in the entry and is not reported # (use CC lines for comments that appear on failure) #################### # Command line tests #################### ID acdc-0001 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0002 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -aint 5 -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0003 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -ai 5 -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0004 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir -sbegin 5 -send 1000 tembl:paamir x.x -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0005 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir -sbegin 5 -send 1000 x.x -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0006 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest -sbegin 5 -send 1000 tembl:paamir tembl:paamir x.x -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0007 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -sbegin 5 -send 1000 -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0008 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x CL -sbegin_asequence 5 -send_asequence 1000 -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-0009 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -sbegin_as 5 -send_as 1000 -auto FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 // ID acdc-ex AP acdc CL antigenic IN tsw:act1_fugru IN IN FI act1_fugru.antigenic FZ = 0 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdlog-check AQ acdlog CL antigenic IN tsw:act1_fugru IN IN FI act1_fugru.antigenic FZ = 0 FI antigenic.acdlog FC = 4888 FP 47 /^acdProcess/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdpretty-ex AP acdpretty PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest FI qatest.acdpretty FZ = 810 FP 3 /^string:/ FP 12 /^[a-z]+: / FI stdout FC = 1 FP /^Created qatest.acdpretty\n/ // ID acdtable-ex AP acdtable CL antigenic FI stderr FC = 49 FP 8 /[<]tr/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdtrace-ex AP acdtrace CL antigenic IN tsw:act1_fugru IN IN FI act1_fugru.antigenic FZ = 0 FI stderr FC = 20 FP 9 /^Trace: +\d+/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdvalid-ex AP acdvalid CL antigenic FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdc-0011 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest -help FI stderr FZ = 932 FP 3 / qualifiers:\n/ FP 4 / qualifiers:/ FP 1 /^ +\[-asequence\] +sequence +Sequence USA\n/ FP 1 /^ +\[-bsequence\] +sequence +Sequence USA\n/ FP 2 /^ +\[-.sequence\] +sequence +Sequence USA\n/ FP / [-]testalen string asequence length \.\.\.\n/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdc-0012 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest -help -verbose FI stderr FZ = 3878 FP 26 / boolean / FP 6 / integer / FP 26 / string / FP / [-]testalen string asequence length \.\.\.\n/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdc-0013 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -debug IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x.x FZ = 0 FI paamir.fasta FZ = 0 FI paamir.out2 FZ = 0 FI qatest.dbg FP /USA to test: 'tembl:paamir'/ FP 2 /^Memory usage / // #################### # ACD parsing errors #################### ID acd-nofile AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL nofile FI stderr FZ > 0 FP /Error: File ../../acd/nofile.acd line 0: ACD file not opened\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noappl AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noappl FI stderr FZ > 0 FP /Error: File .*noappl.acd line 4: Application definition required at start\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-secondappl AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL secondappl FI stderr FZ > 0 FP /Error: File .*secondappl.acd line 9: Application definition allowed only at start\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noleftq AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noleftq FI stderr FZ > 0 FP /Error: File .*noleftq.acd line 7: \(output\) Failed to find '\[' for section output\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noleftsec AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noleftsec FI stderr FZ > 0 FP /Error: File .*noleftsec.acd line 5: \(output\) Failed to find '\[' for section output\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noleftappl AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noleftappl FI stderr FZ > 0 FP /Error: File .*noleftappl.acd line 3: \(noleftappl\) Failed to find '\[' for application noleftappl\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noendsec AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noendsec FI stderr FZ > 0 FP /Error: Section 'output' has no endsection\n/ FP /Error: Section 'input' has no endsection\n/ FP 2 /Error: Section '.*' has no endsection\n/ FP /Error: File .*noendsec.acd line 13: Unclosed sections in ACD file\n/ FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / // ID acd-noquote AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noquote FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noquote.acd line 5: \(outtest\) Unexpected end of file, no closing quote\n/ // ID acd-novalue AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL novalue FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*novalue.acd line 5: \(outtest\) Unexpected end of file, attribute value not found\n/ // ID acd-badstage AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badstage FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badstage.acd line 5: Unrecognized token 'dingsbum'\n/ // ID acd-calcparam AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL calcparam FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*calcparam.acd line 22: [(]outtest[)] 'parameter' attribute cannot use a variable. It is used .* been set\n/ // ID acd-noapplname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noapplname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noapplname.acd line 3: Bad or missing application name '\['\n/ // ID acd-badapplname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badapplname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badapplname.acd line 3: Bad or missing application name 'run[*]123'\n/ // ID acd-noqualname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noqualname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noqualname.acd line 5: Bad or missing qualifier alphabetic name '\['\n/ // ID acd-badqualname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badqualname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badqualname.acd line 5: Bad or missing qualifier alphabetic name 'sequence1'\n/ // ID acd-badalias AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badalias FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badalias.acd line 5: Bad syntax qualifier alias name 'file2'\n/ // ID acd-nocolon AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL nocolon FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*nocolon.acd line 5: Expected ':' not found after 'param'\n/ // ID acd-badendsec AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badendsec FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badendsec.acd line 14: Bad endsection 'fred', current section is 'output'\n/ // ID acd-endsecextra AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL endsecextra FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*endsecextra.acd line 18: Bad endsection 'fred', not in a section\n/ // ID acd-dupname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupname.acd line 14: \(outtest\) Name 'outtest' not unique\n/ // ID acd-dupalias AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupalias FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupalias.acd line 14: \(output\) Name\/Alias 'outtest'\/'output' not unique\n/ // ID acd-ambigtype AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigtype FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*ambigtype.acd line 16: ambiguous acd type seqo \(seqout,seqoutall,seqoutset\)\n/ // ID acd-ambigvar AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigvar tembl:paamir -auto FI stderr FZ > 0 FP 1 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*ambigvar.acd line 9: Failed to resolve variable 'seq'\n/ FP /Warning: ambiguous item seq \(sequence,seqmod\)\n/ // ID acd-undefvar AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL undefvar tembl:paamir -auto FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*undefvar.acd line 7: Variable 'seqmod' not yet defined\n/ // ID acd-leftend AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL leftend FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*leftend.acd line 5: \(outtest\) End of file looking for '\]'\n/ // ID acd-valend AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL valend FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*valend.acd line 5: \(outtest\) End of file looking for '\]'\n/ // ID acd-noattname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noattname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noattname.acd line 5: \(outtest\) Bad or missing attribute name 'requ1red'\n/ // ID acd-dupassoc AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupassoc FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupassoc.acd line 5: \(sbegin\) Associated qualifier 'sbegin' clashes with 'sbegin' in ACD file\n/ // ID acd-dupassocb AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupassocb FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupassocb.acd line 5: \(mybool\) Associated qualifier 'sbegin' clashes with 'mybool'\/'sbegin' in ACD file\n/ // ID acd-wrongattr AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL wrongattr FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*wrongattr.acd line 7: \(outtest\) Attribute 'wanted' unknown\n/ // ID acd-ambigdefattr AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigdefattr tembl:paamir -filter FI stderr FZ > 0 FP 1 /Warning: Ambiguous name/token 'd' \(debug,die\)/ FP 1 /Error: / FP 0 /Died: / FP /Error: File .*ambigdefattr.acd line 3: \(ambigdefattr\) Attribute or qualifier 'd' ambiguous \(debug,die\)\n/ // ID acd-ambigassoc AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigassoc FI stderr FZ > 0 FP 1 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Warning: Ambiguous name/token 'f' \(fformat,fopenfile\)\n/ FP /Error: File .*ambigassoc.acd line 8: \(asequence\) Attribute or qualifier 'f' ambiguous \(fformat,fopenfile\)\n/ // ID acd-mixedcase AP acdpretty PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL mixedcase FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: File .*mixedcase.acd line 16: Automatically converting 'testA' to lower case\n/ FI mixedcase.acdpretty FZ > 0 FP /: testa / FI stdout FC = 1 FP /Created mixedcase.acdpretty\n/ // ID acd-testarray AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testarray FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP 1 /^Error: .*testarray.acd line 8: \(numlist\) Array attribute size: 0 less than 1/ // ID acd-attralias AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalias FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP 1 /^Error: .*testalias.acd line 22: \(hstring\) Attribute 'requ' unknown/ // ## Command line validation tests ## Handling of associated qualifiers ID acdc-badqual AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testassoc tembl:eclaci tembl:paamir -sbegin_a 10 IN IN FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Warning: Ambiguous master qualifier 'a' in sbegin_a \(auto,asequence\)/ FP /Died: Unknown qualifier -sbegin_a/ // ID acdc-ambigqual AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -a 5 -auto ER 1 FI stderr FP 1 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Warning: ambiguous qualifier 'a' \(auto,asequence,aint\)/ FP /Died: Unknown qualifier -a\n/ // ID acdc-missing AP acdc ## . as a parameter is a missing value treated as an empty string PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir . x.x ER 1 FI stderr FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Unable to read sequence ''\n/ FP /Died: qatest terminated: Bad value for '-bsequence' and no prompt\n/ // ID acdc-noprefixvalue AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -auto -nologic=Y ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: 'no' prefix used with value for '-nologic=Y'\n/ // ID acdc-noprefixbad AP acdc ## no nullok attribute for this type PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -auto -nooutdir ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: 'no' prefix invalid for '-nooutdir'\n/ // ID acdc-noprefixbad2 AP acdc ## nullok attribute is false PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -auto -notestalen ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: 'no' prefix invalid for '-notestalen'\n/ // ID acdc-novalue AP acdc ## nullok attribute is false PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -auto -testalen ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: Value required for '-testalen'\n/ // ID acdc-novalue2 AP acdc ## nullok attribute is false PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:paamir tembl:paamir x.x -auto -testalen -testblen ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: Value required for '-testalen' before '-testblen'\n/ // ID acdc-codebad AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_LANGUAGE=bad PP export EMBOSS_LANGUAGE CL qatest -help ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: Bad format in codes file ../../acd/codes.bad after 'defbool "Yes or No"'\n/ // ID acdc-codemissing AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_LANGUAGE=missing PP export EMBOSS_LANGUAGE CL qatest -help FI stderr FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: Code file ..\/..\/acd\/codes.missing not found\n/ // ID acdc-testassoc AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testassoc tembl:eclaci tembl:paamir IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 1113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc2 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send at the start should work on both sequences CL testassoc -send -1001 tembl:eclaci tembl:paamir IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 1167:/ // ID acdc-testassoc3 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send after first sequence should work on first sequence CL testassoc tembl:eclaci -send -1001 tembl:paamir IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc4 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send after second sequence should work on second sequence CL testassoc tembl:eclaci tembl:paamir -send -1001 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 1113:/ FP /Bsequence end 1167:/ // ID acdc-testassoc5 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send after another qualifier should work on all sequences CL testassoc tembl:eclaci tembl:paamir -testc "fred" -send -1001 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 1167:/ // ID acdc-testassoc6 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -send for first sequence CL testassoc tembl:eclaci tembl:paamir -testc "fred" -send1 -1001 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc7 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -send for first sequence CL testassoc -send1 -1001 tembl:eclaci tembl:paamir -testc "fred" IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc8 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -send for first sequence CL testassoc tembl:eclaci tembl:paamir -send1 -1001 -testc "fred" IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc9 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -sformat for first sequence makes -send global CL testassoc tembl:eclaci tembl:paamir -sformat1 embl -send -1001 -testc "fred" IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 1167:/ // ID acdc-toomanyparam AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -sformat for first sequence makes -send global CL testassoc tembl:eclaci tembl:paamir tembl:hsfos IN IN FI stderr FZ > 0 FP /^Error: Argument 'tembl:hsfos' : Too many parameters 3\/2\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acdc-alignbadformat AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalign -aformat fred IN FI stderr FZ > 0 FP /Error: Unknown alignment format 'fred'\n/ FP /Died: Alignment option -test: Validation failed\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-alignbadminseq AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalign IN FI stderr FZ > 0 FP /Error: Alignment format specifies at least 2 sequences, alignment has only 0\n/ FP /Died: Alignment option -test: Validation failed\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-alignbadmaxseq AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalignpair IN FI stderr FZ > 0 FP /Error: Alignment format specifies at most 2 sequences, alignment has 3\n/ FP /Died: Alignment option -test: Validation failed\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-alignbadwidth AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalignok -awidth 9 IN FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: Alignment width \(-awidth=9\) too narrow, reset to 10\n/ FI outfile.testalignok FZ = 0 // ID acdc-funconeof AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL oneof IN thr IN 2 FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP / Pick a number / // ID acdc-funconeoffalse AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL oneof IN two FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: integer value out of range 0 less than \(reset to\) 1\n/ // ID acdc-nodatafile AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL datafile -pepdatafile badname.dat IN FI stderr FZ > 0 FP /Error: Unable to open data file 'badname.dat' for input\n/ FP /Died: datafile terminated: Bad value for '-pepdatafile' and no prompt\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-listambig1 AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN f FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: 'f' is ambiguous \(fa,four,fb,five\)\n/ FP /Error: Bad menu option 'f'\n/ // ID acdc-listambig2 AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN t FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: 't' is ambiguous \(two,three\)\n/ FP /Error: Bad menu option 't'\n/ // ID acdc-listbad AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN x FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: 'x' is not a valid menu option\n/ FP /Error: Bad menu option 'x'\n/ FP /Accepted short codes are: a,b,c,fa,fb\n/ // ID acdc-listmax AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN a,b,c,four FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: Menu allows no more than 3 values\n/ FP /Error: Bad menu option 'a,b,c,four'\n/ // ID acdc-listmin AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: Menu needs 1 value\n/ FP /Error: Bad menu option ''\n/ // ID acdc-reportbadformat AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testreport -rformat fred IN FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Unknown report format 'fred'\n/ FP /Died: Report option -test: Validation failed\n/ // ID acdc-reportbadtaglist AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testreporttags IN FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: Bad report taglist at ' str s=String'\n/ FP /Error: File .*testreporttags.acd line 8: \(test\) Bad tag list for report\n/ // ID acdc-selectambig AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN f FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: 'f' is ambiguous \(four,five\)\n/ FP /Error: Bad select option 'f'\n/ // ID acdc-selectbad AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN x FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: 'x' is not a valid selection list option\n/ FP /Error: Bad select option 'x'\n/ FP /Accepted values are: one,two,three,four,five\n/ // ID acdc-selectmax AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN one,two,thr,four FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: Selection list allows no more than 3 values\n/ FP /Error: Bad select option 'one,two,thr,four'\n/ // ID acdc-selectmax2 AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN 1,2,3,4 FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: Selection list allows no more than 3 values\n/ FP /Error: Bad select option '1,2,3,4'\n/ // ID acdc-selectmin AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: Selection list needs 1 value\n/ FP /Error: Bad select option ''\n/ // ID acdc-retry AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_ACDPROMPTS=2 PP export EMBOSS_ACDPROMPTS CL testselect IN 6 IN 7 FI stderr FZ > 0 FP 0 /Warning: / FP 4 /Error: / FP 1 /Died: / FP 2 /Error: Bad select option '[1-9]'\n/ FP /Died: testselect terminated: Bad value for '-test' and no more retries\n/ // ID acdc-badadvanced AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_ACDPROMPTS=2 PP export EMBOSS_ACDPROMPTS CL testselect -testnum fred IN 5 FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Invalid integer value 'fred'\n/ FP /Died: testselect terminated: Bad value for '-testnum' and no prompt\n/ // ID acdc-badauto AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_ACDPROMPTS=2 PP export EMBOSS_ACDPROMPTS CL testselect -test 6 -auto FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP 1 /Error: Bad select option '[1-9]'\n/ FP /Died: testselect terminated: Bad value for '-test' with -auto defined\n/ // ########################## # .embossrc parsing errors ########################## ID nam-badsummary AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badsummary.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 1 /Died: / FP /Error: File .*\.embossrc line 2: Error\(s\) found in included file .*badsummary.rc\n/ FP /Died: Error\(s\) in configuration files\n/ // ID nam-badtype AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badtype.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 1 /Died: / FP /Error: File .*badtype.rc line 1: Invalid definition type 'this'\n/ FP /Error: File .*badtype.rc line 1: Invalid definition type 'badtype'\n/ FP /Error: File .*\.embossrc line 2: Error\(s\) found in included file .*badtype.rc\n/ // ID nam-badset AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badset.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*badset.rc line 7: Unexpected end of file in SET definition\n/ // ID nam-baddb AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/baddb.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*baddb.rc line 3: Unexpected end of file in DBNAME definition\n/ // ID nam-badresattr AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badresattr.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*badresattr.rc line 3: Bad attribute 'badattr' for resource 'badresource'\n/ // ID nam-badinclude AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badinclude.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: File .*\.embossrc line 2: Failed to open include file '[$]emboss_badfile'\n/ // ID nam-includeagain AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/includeagain.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*includeagain.rc line 3: [$]emboss_badfile already read .. skipping\n/ // ID nam-dbempty AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/dbempty.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 5 /Error: / FP 1 /Died: / FP /Error: File .*dbempty.rc line 3: Database 'empty' has no attributes\n/ FP /Error: File .*dbempty.rc line 3: Database 'empty' has no format definition\n/ FP /Error: File .*dbempty.rc line 3: Database 'empty' has no type definition\n/ FP /Error: File .*dbempty.rc line 3: Database 'empty' has no access method definition\n/ // ID nam-dbunknowns AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/dbunknowns.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 4 /Error: / FP 1 /Died: / FP /Error: File .*dbunknowns.rc line 4: Database 'unknowns' format: 'noformat' unknown\n/ FP /Error: File .*dbunknowns.rc line 4: Database 'unknowns' method: 'notknown' unknown\n/ FP /Error: File .*dbunknowns.rc line 4: Database 'unknowns' type: 'nosuchtype' unknown\n/ // ID nam-rsempty AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/rsempty.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*rsempty.rc line 3: Resource 'empty' has no attributes\n/ // ID nam-dbnoquote AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/dbnoquote.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 4 /Error: / FP 1 /Died: / FP /Error: File .*dbnoquote.rc line 4: '\]' found, unclosed quotes in 'unclosed single quotes'\n/ FP /Error: File .*dbnoquote.rc line 8: '\]' found, unclosed quotes in 'unclosed double quotes'\n/ FP /Error: File .*dbnoquote.rc line 12: '\]' found, unclosed quotes in 'unclosed mixed quotes''\n/ // ####################### # Associated qualifiers ####################### ID qual-ufo AP seqret CL ../../data/hba.fa -feat -ufo ../../data/hba.gff CL -auto -sf fasta ## Fails to set feature type in output GFF FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI hba_human.fasta FC = 4 FP /^>HBA_HUMAN / FI hba_human.gff FC = 158 FP /^##Type Protein HBA_HUMAN\n/ // ID qual-ufo-noid AP seqret CL ../../data/noid.fa -feat -ufo ../../data/hba.gff CL -stdout -auto -sf fasta ## noid.fa has no sequence ID ## This upsets the feature reading ## Error GFF Group field for table '' FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^>EMBOSS_001/ // ID qual-ufo-noid-id AP seqret CL ../../data/noid.fa -feat -ufo ../../data/hba.gff CL -stdout -auto -sf fasta -sid fred ## noid.fa has no sequence ID ## This upsets the feature reading ## Error GFF Group field for table '' FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^>fred / // ID qual-sid AP seqret CL ../../data/noid.fa CL -stdout -auto -sf fasta -sid fred ## Fails to use -sid in the output FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^>fred/ // ID qual-sid2 AP seqret CL ../../data/noid.fa CL -stdout -auto -sf fasta -sid fred -osf ncbi ## Fails to use -sid in the output FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^>fred/ // ID qual-sdb AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -sdb fred ## noid.fa has no sequence ID ## This upsets the feature reading ## Error GFF Group field for table '' FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>HBA_HUMAN/ // ID qual-sdb2 AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -sdb fred -osf ncbi ## noid.fa has no sequence ID ## This upsets the feature reading ## Error GFF Group field for table '' FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>gnl[|]fred[|]HBA_HUMAN / // ID qual-osdb AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -osdb fred FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>fred:HBA_HUMAN / // ID qual-osdb2 AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -osdb fred -osf ncbi FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>gnl[|]fred[|]HBA_HUMAN / // ID qual-osdb3 AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -sdb jim -osdb fred -osf ncbi FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>gnl[|]fred[|]HBA_HUMAN / // ################### # Main applications ################### ID aaindexextract-keep AP aaindexextract DL keep PP mkdir ./AAINDEX PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/aaindex1.test FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI AAINDEX DF kytj820101 // ID abiview-ex AP abiview CL -graph cps IN ../../data/abiview.abi IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created abiview.ps\n/ FI abiview.fasta FP /^GNNNNNNNNNG/ FZ = 876 FI abiview.ps FP /^%%Title: PLplot Graph\n/ // ##ID abiview-old ##AP abiview ##CC Example file missing test/data/ba16d2.s1 ##CL -graph ps ##IN ../../data/ba16d2.s1 ##IN ##FI stderr ##FC = 2 ##FI stdout ##FZ = 18 ##FP /^Created abiview.ps\n/ ##FI outfile.fasta ##FZ = 0 ##// ID antigenic-command AP antigenic CL tsw:amir_pseae -auto FI amir_pseae.antigenic FP /^# Program: antigenic\n/ FP /Sequence: AMIR_PSEAE/ FP /246/ FP /1[.]246/ FP / NS.[^P]GSL/ FZ > 100 FC > 5 // ID antigenic-ex AP antigenic IN tsw:act1_fugru IN IN FI act1_fugru.antigenic FP /^# Program: antigenic\n/ FP /1[.]207/ FP /AA[^AV]VV/ FZ > 100 FC > 5 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID antigenic-ex2 UC By using the '-rformat gff' qualifier, a GFF file of the predicted regions can be produced. AP antigenic CL -rformat gff IN tsw:act1_fugru IN IN FI act1_fugru.antigenic FP /^##Type Protein ACT1_FUGRU\n/ FZ > 100 FC > 5 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID backtranseq-ex UC Note that this is a human protein and so the default human codon frequency file is used ie. is not specified AP backtranseq IN tsw:opsd_human IN FI opsd_human.fasta FP /^>OPSD_HUMAN/ FP /CGCCACCGGCGTGGTG\n/ FZ = 1092 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID backtranseq-ex2 UC This uses a drosophila sequence and codon table. AP backtranseq CL -cfile Edrome.cut IN tsw:ach2_drome IN FI ach2_drome.fasta FP /^>ACH2_DROME/ FP /GAGAAGAAGAAC\n/ FZ = 1838 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID banana-data AP banana CL -outfile banana.data -nograph IN tembl:rnu68037 FI banana.data FC = 1219 FP /c 17.7 20.0\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID banana-ex AP banana CL -nooutfile -graph ps IN tembl:rnu68037 FI stdout FC = 1 FP /^Created banana.ps\n/ FI banana.ps FC > 1 FP /%%Title: PLplot Graph\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID banana-ex2 AP banana CL -graph data IN tembl:rnu68037 FI banana.profile FZ = 25601 FP /^a +0.0 +0.0\nt +19.7 +0.0\ng +17.7 +0.0\na +21.1 +0.0\n/ FP /^a +14.9 +0.0\nc +17.7 +20.0\nc +15.7 +19.2\nt +15.7 +18.5\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 9 FP /^Created banana1.dat\n/ FI banana1.dat FC > 1 FP /^##/ FI banana2.dat FC > 1 FP /^##/ FI banana3.dat FC > 1 FP /^##/ FI banana4.dat FC > 1 FP /^##/ FI banana5.dat FC > 1 FP /^##/ FI banana6.dat FC > 1 FP /^##/ FI banana7.dat FC > 1 FP /^##/ FI banana8.dat FC > 1 FP /^##/ FI banana9.dat FC > 1 FP /^##/ // ID biosed-ex UC Replace all 'T's with 'U's to create an RNA sequence AP biosed CL tembl:hsfau hsfau.rna -target T -replace U FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.rna FZ = 562 FP /^UCUAAUAAAAAAGCCACUUAGUUCAGUCAAAAAAAAAA\n/ // ID biosed-ex2 UC Replace all 'PPP' protein motifs with 'XXPPPXX' AP biosed CL tsw:AMIR_PSEAE AMIR_PSEAE.pep -target PPP -replace XXPPPXX FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI AMIR_PSEAE.pep FZ = 252 FP /^MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWXXPPPXXEAFDVPVDVV\n/ // ID btwisted-ex AP btwisted CL -auto tembl:ab000095 -sbegin 100 -send 120 FI ab000095.btwisted FP /^# Twisting calculated from 100 to 120 of AB000095\n/ FP /^Total twist \(degrees\): 681\.1\n/ FP /^Total turns : 1\.89\n/ FP /^Average bases per turn: 11\.10\n/ FP /^Total stacking energy : -179\.34\n/ FP /^Average stacking energy per dinucleotide: -8\.97\n/ // ID cai-ex AP cai CL TEMBL:AB009602 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ab009602.cai FP /0[.]188/ // ID chaos-ex AP chaos CL tembl:eclac -graph cps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI chaos.ps FZ > 100 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 17 FP /^Created chaos.ps\n/ // ID chaos-data AP chaos CL tembl:eclac -graph data FI stdout FC = 1 FP /^Created chaos1.dat\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI chaos1.dat FC = 7493 FP /^##Screen x1 -0.100000 y1 -0.100000 x2 1.400000 y2 1.100000\n/ FP /^Line x1 0.090456 y1 0.242971 x2 0.090556 y2 0.242971 colour 0\n/ FP /^Text3 x1 0.000000 y1 0.000000 colour 0 size 1.000000 A\n/ FP /^Text1 x1 1.100000 y1 0.750000 colour 0 size 0.500000 A 1739\n/ FP /^Text1 x1 1.100000 y1 0.450000 colour 0 size 0.500000 [%]A 23.26\n/ // ID charge-ex AP charge CL tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hbb_human.charge FP /CHARGE of HBB_HUMAN from 1 to 146: window 5/ FC = 145 // ID checktrans-ex AP checktrans IN ../../data/paamir.pep IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir_1.checktrans FZ = 132 FP /Total STOPS:\s+7\n/ FP /^\s+7\s+635\s+357\s+278-634\s+PAAMIR_1_7\n/ FI paamir_1.fasta FZ = 375 FP /\A>PAAMIR_1_7\n/ FP /^PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR\n/ FI paamir_1.gff FZ = 133 FP /^PAAMIR_1.*278\t634\t0\.000/ // ID chips-ex AP chips CL -sbeg 135 -send 1292 IN tembl:paamir IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.chips FP /Nc = 32[.]951/ // ID cirdna-ex AP cirdna CL -graph cps IN ../../data/data.cirp IN IN IN IN FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI cirdna.ps FZ = 23067 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 18 FP /^Created cirdna.ps\n/ // ID codcmp-ex UC This compares the codon usage tables for Escherichia coli and Haemophilus influenzae. AP codcmp IN Eecoli.cut IN Ehaein.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.codcmp FP /^Mean Squared Difference = 0[.]034\n/ FP /^Sum Squared Difference = 2[.]178\n/ FP /^Root Mean Squared Difference = 0[.]184\n/ FP /^Sum Difference = 9[.]504\n/ FP /^Mean Difference = 0[.]149\n/ FP /^Codons not appearing = 0\n/ // ID codcopy-ex AP codcopy IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 75 FP 64 /^[ACGT][ACGT][ACGT]/ // ID coderet-ex UC To extract all of the CDS, mRNA and the protein translations: AP coderet IN tembl:X03487 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsferg1.fasta FP /^>x03487_cds_1\natgacgaccgcgt/ FP /aatgaaagctaa\n>x03487_mrna_1\ncagacgttcttcgc/ FP /ctcctacgtttacctgtccatg\n>x03487_pro_1\nMTTASTSQVRQNY/ FI hsferg1.coderet FC = 3 FP / 1 1 1 3 HSFERG1\n/ // ID coderet-ex2 UC To only extract the mRNA sequence: AP coderet CL -nocds -notranslation IN tembl:X03487 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsferg1.fasta FP 0 /^>x03487_cds_1/ FP /^>x03487_mrna_1\ncagacgttcttcgc/ FP 0 /^>x03487_pro_1/ FI hsferg1.coderet FC = 3 FP / 1 1 HSFERG1\n/ // ID compseq-ex UC To count the frequencies of dinucleotides in a file: AP compseq CL tembl:hsfau 2 result3.comp FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result3.comp FZ = 912 FP /^Total count\s+517\n/ FP /^AA\s+45\s+0\.0870406\s+0\.0625000\s+1\.3926499\n/ // ID compseq-ex2 UC To count the frequencies of hexanucleotides, without outputting the results of hexanucleotides that do not occur in the sequence: AP compseq CL tembl:hsfau 6 result6.comp -nozero FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result6.comp FZ = 18689 FP /^Total count\s+513\n/ FP /^AAAAAA\s+6\s+0\.0116959\s+0\.0002441\s+47\.9064327\n/ // ID compseq-ex3 UC To count the frequencies of trinucleotides in frame 2 of a sequence and use a previously prepared compseq output to show the expected frequencies: AP compseq CL tembl:hsfau 3 result3.comp -frame 2 -in ../../data/prev.comp FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result3.comp FZ = 2697 FP /^Total count\s+172\n/ FP /^AAA\s+7\s+0\.0406977\s+0\.0329457\s+1\.2352955\n/ // ID cons-ex AP cons IN ../../data/dna.msf IN aligned.cons FI stderr FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FC = 2 FI aligned.cons FZ = 134 FP /\A>EMBOSS_001\n/ FP /^ACGTACGTACGTACGTACGTnnnnACGTACGTACGTACGTnnnnnnnnnnnnnnnnnnnn\n/ FP /^nnnnnnnnnnnnnnnnnnnnACGTACGTACGTACGTACGTACGTACGTnnnnACGTACGT\n/ // ID cpgplot-ex AP cpgplot CL tembl:rnu68037 -graph cps IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created cpgplot.ps\n/ FI rnu68037.cpgplot FP /RNU68037 from 1 to 1218/ FP /Observed\/Expected ratio > 0\.60/ FP /Length 406 \(104\.\.509\)/ FP /Length 329 \(596\.\.924\)/ FI rnu68037.gff FP /^##Type DNA RNU68037/ FI cpgplot.ps FP /^%%Title: PLplot Graph/ // ID cpgplot-old AP cpgplot CL tembl:rnu68037 -graph data IN IN IN IN IN IN FI stdout FC = 3 FP /^Created cpgplot3.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rnu68037.cpgplot FP /RNU68037 from 1 to 1218/ FP /Observed\/Expected ratio > 0\.60/ FP /Length 406 \(104\.\.509\)/ FP /Length 329 \(596\.\.924\)/ FI rnu68037.gff FZ = 196 FP /^RNU68037.*\t104\t509\t/ FP /^RNU68037.*\t596\t924\t/ FI cpgplot1.dat FZ = 24885 FP /^444\.000000\s+1\.066856\n/ FI cpgplot2.dat FZ = 25999 FP /^444\.000000\s+75\.000000\n/ FI cpgplot3.dat FZ = 24883 FP /^444\.000000\s+1\.000000\n/ // ID cpgreport-ex AP cpgreport CL tembl:rnu68037 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rnu68037.cpgreport FP /CPGREPORT of RNU68037 from 1 to 1218/ FP /RNU68037 12 13 17 1 100\.0 -/ FP /RNU68037 1183 1193 26 2 72\.7 2\.00/ FI rnu68037.gff FZ = 497 FP /^RNU68037\tcpgreport\tmisc_feature\t96\t1032\t630\.000\t/ // ID cusp-ex UC This example uses only one input sequence. The normal use would be to use a set of coding sequences as the input. AP cusp CL -sbeg 135 -send 1292 IN tembl:paamir IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.cusp FP /GCA +A +0\.077 +7\.772 +3/ FP /GCC +A +0\.462 +46\.632 +18/ FP /GCG +A +0\.462 +46\.632 +18/ FP /GCT +A +0\.000 +0\.000 +0/ // ID cutgextract-keep AP cutgextract DL keep PP mkdir CODONS PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI CODONS FI outfile.cutgextract FC = 9 FP 9 /^Writing .*[.]cut/ // ID cutgextract-species AP cutgextract DL keep PP mkdir CODONS PP EMBOSS_DATA=./ PP export EMBOSS_DATA CL -species "Aedes *" IN ../../data IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI CODONS FI outfile.cutgextract FC = 3 FP 3 /^Writing .*[.]cut/ // ID cutgextract-outfile AP cutgextract DL keep PP mkdir CODONS PP EMBOSS_DATA=./ PP export EMBOSS_DATA CL -species "Aedes *" -filename EAedes IN ../../data IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI CODONS FI outfile.cutgextract FC = 1 FP 1 /^Writing EAedes[.]cut/ // ID cutseq-ex UC To remove bases 10 to 12 from a database entry and write to the new sequence file 'gatta2.seq': AP cutseq CL tembl:paamir gatta2.seq -from=10 -to=12 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI gatta2.seq FZ = 2293 FP /^ggtaccgctcgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgatcta\n/ // ID cutseq-ex2 UC To remove the first 20 bases from 'tembl:paamir' and write it to 'jsh.seq': AP cutseq CL tembl:paamir -from=1 -to=20 -out=jsh.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI jsh.seq FZ = 2275 FP /^tgctcgatcaccaccagccgggcgacgggaactgcacgatctacctggcgagcctggagc\n/ // ID cutseq-ex3 UC If the default start and end positions are accepted, then all of the sequence is removed! AP cutseq CL tembl:paamir starta.seq -sbeg=-1000 -send=1290 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI starta.seq FZ = 92 FP /\A>PAAMIR X13776[.]1 .* regulation\Z/ // ID dan-ex AP dan IN tembl:paamir IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.dan FZ = 170172 FP / +1 +20 +64\.9 +70\.0 .* ggtaccgctggccgagcatc *\n/ FP / +2 +21 +63\.7 +65\.0 .* gtaccgctggccgagcatct *\n/ FC = 2165 // ID dan-ex2 UC An example of producing a plot of Tm: AP dan CL -plot -graph cps IN tembl:paamir IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 15 FP /^Created dan.ps\n/ FI dan.ps FP /^%%Title: PLplot Graph/ FI paamir.dan FZ = 0 // ID dan-old UC An example of producing a plot of Tm: AP dan CL -plot -graph data IN tembl:paamir IN IN IN IN IN FI stdout FC = 1 FP /^Created dan1.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dan1.dat FZ = 46560 FP /^11\.000000\s+64\.921204\n/ FP /^2158\.000000\s+62\.373310\n/ FI paamir.dan FZ = 0 // ############################################# # Direct access database(s) ############################################# ID direct-all AP seqret CL temblall:* test.out -auto FI test.out FP 44 /^>/ // ID direct-filename AP seqret CL temblvrt:* test.out -auto FI test.out FP 25 /^>/ // ID direct-exclude AP seqret CL temblrest:* test.out -auto FI test.out FP 19 /^>/ // ############################################# # The qapblast database(s) ############################################# ID dbiblast-allsys-keep DL keep AP dbiblast CL -fields "acnum,seqvn,des" IN swnew IN ../../data IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000swnew.pin\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ FI des.hit FZ = 576 FP /\A.{300}\006/ FI des.trg FZ = 1839 FP /\A.{308}1\000/ FI seqvn.hit FZ = 300 FP /\A.{300}$/ FI seqvn.trg FZ = 300 FP /\A.{300}$/ // ID dbiblast-allnosys-keep DL keep AP dbiblast CL -fields "acnum,seqvn,des" -nosystemsort IN swnew IN ../../data IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000swnew.pin\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ FI des.hit FZ = 576 FP /\A.{300}\006/ FI des.trg FZ = 1839 FP /\A.{308}1\000/ FI seqvn.hit FZ = 300 FP /\A.{300}$/ FI seqvn.trg FZ = 300 FP /\A.{300}$/ // ID dbiblast-nosys-keep DL keep AP dbiblast CL -nosystemsort IN swnew IN ../../data IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000swnew.pin\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ // ID dbiblast-ex-keep UC This creates EMBOSS indices for the BLAST database 'swnew' DL keep AP dbiblast IN swnew IN ../../data IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000swnew.pin\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ // ID dbiblast-idfirst AP seqret CL qapblast-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiblast-idsecond AP seqret CL qapblast-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbiblast-last AP seqret CL qapblast-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbiblast-nextlast AP seqret CL qapblast-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbiblast-acfirst AP seqret CL qapblast-acc:P53450 test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU P53450 / FP 1 /^>/ // ID dbiblast-acsecond AP seqret CL qapblast-acc:P79755 test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU P79755 / FP 1 /^>/ // ID dbiblast-aclast AP seqret CL qapblast-acc:Q90515 test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU Q90515 / FP 1 /^>/ // ID dbiblast-all AP seqret CL qapblast:* test.out -auto FI test.out FZ = 4474 FP 1 /^>TM21_FUGRU Q90515 / FP 9 /^>/ // ID dbiblast-wild AP seqret CL qapblast:n* test.out -auto FI test.out FZ = 516 FP 2 /^>N/ FP 2 /^>/ // ############################################# # The qapblastsplit database(s) ############################################# ID dbiblast-split-keep DL keep AP dbiblast IN swsplit IN ../../data IN swsplit.*.pin IN IN IN P IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 410 FP /\A.{300}\001\000swsplit.00.pin\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ // ID dbiblast-split-wild-keep DL keep AP dbiblast IN swsplit IN ../../data IN swsplit.*.* IN IN IN P IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 410 FP /\A.{300}\001\000swsplit.00.pin\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ // ID dbiblast-split-list-keep DL keep AP dbiblast IN swsplit IN ../../data IN swsplit.00.pin swsplit.01.pin swsplit.02.pin swsplit.03.pin swsplit.04.pin IN IN IN P IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 410 FP /\A.{300}\001\000swsplit.00.pin\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ // ID dbiblast-split-idfirst AP seqret CL qapblastsplit-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiblast-split-idsecond AP seqret CL qapblastsplit-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbiblast-split-last AP seqret CL qapblastsplit-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbiblast-split-nextlast AP seqret CL qapblastsplit-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbiblast-split-acfirst AP seqret CL qapblastsplit-acc:P53450 test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU P53450 / FP 1 /^>/ // ID dbiblast-split-acsecond AP seqret CL qapblastsplit-acc:P79755 test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU P79755 / FP 1 /^>/ // ID dbiblast-split-aclast AP seqret CL qapblastsplit-acc:Q90515 test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU Q90515 / FP 1 /^>/ // ID dbiblast-split-all AP seqret CL qapblastsplit:* test.out -auto FI test.out FZ = 4474 FP 1 /^>TM21_FUGRU Q90515 / FP 9 /^>/ // ID dbiblast-split-wild AP seqret CL qapblastsplit:n* test.out -auto FI test.out FZ = 516 FP 2 /^>N/ FP 2 /^>/ // ID dbiblast-split-testexc AP seqret CL qapblastsplitexc:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiblast-split-testexcall AP seqret CL qapblastsplitexc:* test.out -auto FI test.out FZ = 3864 FP 1 /^>CO9_FUGRU / FP 7 /^>/ // ID dbiblast-split-testexcfail ER 1 AP seqret CL qapblastsplitexc:FABP_FUGRU test.out -auto FI stderr FZ = 131 FP /Error: Unable to read sequence 'qapblastsplitexc:FABP_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbiblast-split-testinc AP seqret CL qapblastsplitinc:FABP_FUGRU test.out -auto FI test.out FZ = 175 FP 1 /^>FABP_FUGRU / FP 1 /^>/ // ID dbiblast-split-testincall AP seqret CL qapblastsplitinc:* test.out -auto FI test.out FZ = 610 FP 1 /^>FABP_FUGRU / FP 2 /^>/ // ID dbiblast-split-testincfail ER 1 AP seqret CL qapblastsplitinc:CO9_FUGRU test.out -auto FI stderr FZ = 130 FP /Error: Unable to read sequence 'qapblastsplitinc:CO9_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qanfasta database ############################################# ID dbifasta-ex-keep DL keep AP dbifasta IN EMROD IN idacc IN ../../data IN emrod IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000emrod\000/ FI entrynam.idx FZ = 354 FP /\A.{300}MMAM\000/ FI acnum.hit FZ = 312 FP /\A.{300}\001/ FI acnum.trg FZ = 342 FP /\A.{308}L48662\001/ // ID dbifasta-allsys-keep DL keep AP dbifasta CL -fields="acnum,seqvn,des" IN EMROD IN idacc IN ../../data IN emrod IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000emrod\000/ FI entrynam.idx FZ = 354 FP /\A.{300}MMAM\000/ FI acnum.hit FZ = 312 FP /\A.{300}\001/ FI acnum.trg FZ = 342 FP /\A.{308}L48662\001/ FI seqvn.hit FZ = 300 FP /\A.{44} +/ FI seqvn.trg FZ = 300 FP /\A.{44} +/ FI des.hit FZ = 412 FP /\A.{300}\001/ FP /\A.{44} +/ FI des.trg FZ = 750 FP /\A.{308}11\000/ FP /\A.{44} +/ // ID dbifasta-allnosys-keep DL keep AP dbifasta CL -fields="acnum,seqvn,des" -nosystemsort IN EMROD IN idacc IN ../../data IN emrod IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000emrod\000/ FI entrynam.idx FZ = 354 FP /\A.{300}MMAM\000/ FI acnum.hit FZ = 312 FP /\A.{300}\001/ FI acnum.trg FZ = 342 FP /\A.{308}L48662\001/ FI seqvn.hit FZ = 300 FP /\A.{44} +/ FI seqvn.trg FZ = 300 FP /\A.{44} +/ FI des.hit FZ = 412 FP /\A.{300}\001/ FP /\A.{44} +/ FI des.trg FZ = 750 FP /\A.{308}11\000/ FP /\A.{44} +/ // ID dbifasta-idfirst AP seqret CL qanfasta-id:MMAM test.out -auto FI test.out FZ = 471 FP 1 /^>MMAM / FP 1 /^>/ // ID dbifasta-idsecond AP seqret CL qanfasta-id:RNOPS test.out -auto FI test.out FZ = 1565 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbifasta-last AP seqret CL qanfasta-id:RNU68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>RNU68037 / FP 1 /^>/ // ID dbifasta-nextlast AP seqret CL qanfasta-id:RNOPS test.out -auto FI test.out FZ = 1565 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbifasta-all AP seqret CL qanfasta:* test.out -auto FI test.out FZ = 3354 FP 1 /^>RNOPS / FP 3 /^>/ // ID dbifasta-wild AP seqret CL qanfasta:r* test.out -auto FI test.out FZ = 2883 FP 1 /^>RNOPS / FP 2 /^>R/ FP 2 /^>/ // ############################################# # The qapfasta database ############################################# ID dbifasta-swiss-keep DL keep AP dbifasta IN SWNEW IN idacc IN ../../data IN swnew IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000swnew\000/ FI entrynam.idx FZ = 480 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP /\A.{300}\006/ FI acnum.trg FZ = 426 FP /\A.{308}O42493\001/ // ID dbifasta-swiss-idfirst AP seqret CL qapfasta-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-idsecond AP seqret CL qapfasta-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-last AP seqret CL qapfasta-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-nextlast AP seqret CL qapfasta-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-all AP seqret CL qapfasta:* test.out -auto FI test.out FZ = 4474 FP 1 /^>E2BB_FUGRU / FP 9 /^>/ // ID dbifasta-swiss-wild AP seqret CL qapfasta:n* test.out -auto FI test.out FZ = 516 FP 1 /^>NEUI_FUGRU / FP 2 /^>N/ FP 2 /^>/ // ############################################# # The qawfasta database ############################################# ID dbifasta-worm-keep DL keep AP dbifasta IN WORM IN simple IN ../../data IN wormpep.clone.* IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 344 FP /\A.{300}\001\000wormpep.clone.AB\000/ FI entrynam.idx FZ = 1488 FP /\A.{300}AC3[.]1\000/ FI acnum.hit FZ = 564 FP /\A.{300}\001/ FI acnum.trg FZ = 1356 ## Pattern needs 's' modifier ... binary data includes a newline FP s /\A.{308}AC3[.]1\000/ // ID dbifasta-worm-idfirst AP seqret CL qawfasta-id:AC3.1 test.out -auto FI test.out FZ = 426 FP 1 /^>AC3[.]1 / FP 1 /^>/ // ID dbifasta-worm-idsecond AP seqret CL qawfasta-id:AC3.2 test.out -auto FI test.out FZ = 1057 FP 1 /^>AC3[.]2 / FP 1 /^>/ // ID dbifasta-worm-last AP seqret CL qawfasta-id:ZK637.15 test.out -auto FI test.out FZ = 205 FP 1 /^>ZK637[.]15 / FP 1 /^>/ // ID dbifasta-worm-nextlast AP seqret CL qawfasta-id:zk637.14 test.out -auto FI test.out FZ = 260 FP 1 /^>ZK637[.]14 / FP 1 /^>/ // ID dbifasta-worm-all AP seqret CL qawfasta:* test.out -auto FI test.out FZ = 33816 FP 66 /^>/ // ID dbifasta-worm-wild AP seqret CL qawfasta:a* test.out -auto FI test.out FZ = 19764 FP 40 /^>A[^\n]+\n[^>]/ FP 40 /^>/ // ID dbifasta-worm-wildz AP seqret CL qawfasta:z* test.out -auto FI test.out FZ = 7264 FP 15 /^>Z[^\n]+\n[^>]/ FP 15 /^>/ // ############################################# # The qanflat database ############################################# ID dbiflat-ex-keep DL keep AP dbiflat IN EMBL IN EMBL IN ../../embl IN rod.dat IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000rod\.dat\000/ FI entrynam.idx FZ = 354 FP /\A.{300}MMAM\000/ FI acnum.hit FZ = 312 FP /\A.{300}\001/ FI acnum.trg FZ = 342 FP /\A.{308}L48662\001/ // ID dbiflat-nosys-keep DL keep AP dbiflat CL -nosystemsort IN EMBL IN EMBL IN ../../embl IN rod.dat IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP /\A.{300}\001\000rod\.dat\000/ FI entrynam.idx FZ = 354 FP /\A.{300}MMAM\000/ FI acnum.hit FZ = 312 FP /\A.{300}\001/ FI acnum.trg FZ = 342 FP /\A.{308}L48662\001/ // ID dbiflat-id AP seqret CL qanflat-id:rnops test.out -auto FI test.out FZ = 1567 FP /\A>RNOPS / FP 1 /^>/ // ID dbiflat-idfirst AP seqret CL qanflat-id:MMAM test.out -auto FI test.out FZ = 473 FP 1 /^>MMAM / FP 1 /^>/ // ID dbiflat-idsecond AP seqret CL qanflat-id:RNOPS test.out -auto FI test.out FZ = 1567 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbiflat-last AP seqret CL qanflat-id:RNU68037 test.out -auto FI test.out FZ = 1320 FP 1 /^>RNU68037 / FP 1 /^>/ // ID dbiflat-nextlast AP seqret CL qanflat-id:RNOPS test.out -auto FI test.out FZ = 1567 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbiflat-all AP seqret CL qanflat:* test.out -auto FI test.out FZ = 3360 FP 1 /^>RNOPS / FP 3 /^>/ // ID dbiflat-wild AP seqret CL qanflat:r* test.out -auto FI test.out FZ = 2887 FP 1 /^>RNOPS / FP 2 /^>/ // ID dbiflat-tembl-idfirst AP seqret CL tembl-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbiflat-tembl-idsecond AP seqret CL tembl-id:AB000360 test.out -auto FI test.out FZ = 2685 FP 1 /^>AB000360 / FP 1 /^>/ // ID dbiflat-tembl-last AP seqret CL tembl-id:XLRHODOP test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbiflat-tembl-nextlast AP seqret CL tembl-id:XL23808 test.out -auto FI test.out FZ = 4876 FP 1 /^>XL23808 / FP 1 /^>/ // ID dbiflat-tembl-multiacc AP seqret CL tembl-acc:V00451 test.out -auto FI test.out FZ = 6261 FP 3 /^>GM/ FP 3 /^>/ // ID dbiflat-tembl-all AP seqret CL tembl:* test.out -auto FI test.out FZ = 540075 FP 3 /^>GM/ FP 44 /^>/ // ID dbiflat-tembl-wild AP seqret CL tembl:h* test.out -auto FI test.out FZ = 154591 FP 5 /^>HSF/ FP 16 /^>/ // ############################################# # The qapflat database ############################################# ID dbiflat-swiss-keep DL keep AP dbiflat IN SWNEW IN IN ../../swnew IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 366 FP /\A.{300}\001\000new_seq\.dat\000/ FI entrynam.idx FZ = 400 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 320 FP /\A.{300}\003/ FI acnum.trg FZ = 370 FP /\A.{308}P53450\001/ // ID dbiflat-swiss-allsys-keep DL keep AP dbiflat CL -fields="acnum,seqvn,des,keyword,taxon" IN SWNEW IN IN ../../swnew IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 366 FP /\A.{300}\001\000new_seq\.dat\000/ FI entrynam.idx FZ = 400 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 320 FP /\A.{300}\003/ FI acnum.trg FZ = 370 FP /\A.{308}P53450\001/ FI des.trg FZ = 1326 FP /\A.{308}1\000/ FI des.hit FZ = 468 FP /\A.{300}\004/ FI keyword.trg FZ = 1200 FP /\A.{308}ACYLTRANSFERASE\000/ FI keyword.hit FZ = 408 FP /\A.{300}\004/ FI seqvn.trg FZ = 380 FP /\A.{308}P53450[.]0\001/ FI seqvn.hit FZ = 320 FP /\A.{300}\003/ FI taxon.trg FP /\A.{308}ACTINOPTERYGII\000/ FZ = 624 FI taxon.hit FZ = 540 FP /\A.{300}\001/ // ID dbiflat-swiss-allnosys-keep DL keep AP dbiflat CL -nosystemsort -fields="acnum,seqvn,des,keyword,taxon" IN SWNEW IN IN ../../swnew IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 366 FP /\A.{300}\001\000new_seq\.dat\000/ FI entrynam.idx FZ = 400 FP /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 320 FP /\A.{300}\003/ FI acnum.trg FZ = 370 FP /\A.{308}P53450\001/ FI des.trg FZ = 1326 FP /\A.{308}1\000/ FI des.hit FZ = 468 FP /\A.{300}\004/ FI keyword.trg FZ = 1200 FP /\A.{308}ACYLTRANSFERASE\000/ FI keyword.hit FZ = 408 FP /\A.{300}\004/ FI seqvn.trg FZ = 380 FP /\A.{308}P53450[.]0\001/ FI seqvn.hit FZ = 320 FP /\A.{300}\003/ FI taxon.trg FZ = 624 FP /\A.{308}ACTINOPTERYGII\000/ FI taxon.hit FZ = 540 FP /\A.{300}\001/ // ID dbiflat-swiss-idfirst AP seqret CL qapflat-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-idsecond AP seqret CL qapflat-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-last AP seqret CL qapflat-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-nextlast AP seqret CL qapflat-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-all AP seqret CL qapflat:* test.out -auto FI test.out FZ = 2413 FP 1 /^>ODO2_FUGRU / FP 5 /^>/ // ID dbiflat-swiss-wild AP seqret CL qapflat:o* test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-testexc AP seqret CL qapflatexc-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-testexcall AP seqret CL qapflatexc-id:* test.out -auto FI test.out FZ = 1978 FP 1 /^>CO9_FUGRU / FP 4 /^>/ // ID dbiflat-swiss-testexcfail ER 1 AP seqret CL qapflatexc-id:FOS_FUGRU test.out -auto FI stderr FZ = 127 FP /Error: Unable to read sequence 'qapflatexc-id:FOS_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbiflat-swiss-testinc AP seqret CL qapflatinc-id:FOS_FUGRU test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-testincall AP seqret CL qapflatinc-id:* test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU / FP 1 /^>/ // ID dbiflat-swiss-testincfail ER 1 AP seqret CL qapflatinc-id:CO9_FUGRU test.out -auto FI stderr FZ = 127 FP /Error: Unable to read sequence 'qapflatinc-id:CO9_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbiflat-genbank-keep DL keep AP dbiflat IN GENBANK IN GENBANK IN ../../genbank IN *.seq IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 520 ## Pattern needs 's' modifier ... binary data includes a newline FP s /\A.{300}\001\000gbbct1.seq\000/ FI entrynam.idx FZ = 1080 FP /\A.{300}AB000095\000/ FI acnum.hit FZ = 624 FP /\A.{300}\001/ FI acnum.trg FZ = 1596 FP /\A.{308}AB000095\001/ // ############################################# # The qangcg database(s) ############################################# ID dbigcg-ex-keep DL keep TI 120 AP dbigcg IN EMBL IN EMBL IN ../../embl IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 606 FP /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/ FI entrynam.idx FZ = 1020 FP /\A.{300}AB000095/ FI acnum.hit FZ = 492 FP /\A.{300}\001/ FI acnum.trg FZ = 1068 FP /\A.{308}AB000095/ // ID dbigcg-id AP seqret CL qangcg-id:hsfau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbigcg-idfirst AP seqret CL qangcg-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbigcg-idsecond AP seqret CL qangcg-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbigcg-last AP seqret CL qangcg-id:XLRHODOP test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbigcg-acc AP seqret CL qangcg:L07770 test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbigcg-nextlast AP seqret CL qangcg-id:XL23808 test.out -auto FI test.out FZ = 4876 FP 1 /^>XL23808 / FP 1 /^>/ // ID dbigcg-splitfirst AP seqret CL qangcg-id:CEY39B6 test.out -auto FI test.out FZ = 362911 FP 1 /^>CEY39B6 / FP 1 /^>/ // ID dbigcg-splitmid AP seqret CL qangcg-id:PFMAL4P1 test.out -auto FI test.out FZ = 399267 FP 1 /^>PFMAL4P1 / FP 1 /^>/ // ID dbigcg-splitbefore AP seqret CL qangcg-id:AC017364 test.out -auto FI test.out FZ = 3801 FP 1 /^>AC017364 / FP 1 /^>/ // ID dbigcg-splitafter AP seqret CL qangcg-id:PFMAL4P3 test.out -auto FI test.out FZ = 326444 FP 1 /^>PFMAL4P3 / FP 1 /^>/ // ID dbigcg-splitend AP seqret CL qangcg-id:ECUW67 test.out -auto FI test.out FZ = 378731 FP 1 /^>ECUW67 / FP 1 /^>/ // ID dbigcg-all AP seqret CL qangcg:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbigcg-wild AP seqret CL qangcg:h* test.out -auto FI test.out FZ = 77403 FP 13 /^>H/ FP 13 /^>/ // ID dbigcg-testexc AP seqret CL qangcgexc-id:hsfau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbigcg-testexcall AP seqret CL qangcgexc-id:* test.out -auto FI test.out FZ = 1744803 FP 1 /^>HSFAU / FP 30 /^>/ // ID dbigcg-testexcfail ER 1 AP seqret CL qangcgexc-id:eclac test.out -auto FI stderr FZ = 122 FP /Error: Unable to read sequence 'qangcgexc-id:eclac'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbigcg-testinc AP seqret CL qangcginc-id:eclac test.out -auto FI test.out FZ = 7676 FP 1 /\A>ECLAC / FP 1 /^>/ // ID dbigcg-testincall AP seqret CL qangcginc-id:* test.out -auto FI test.out FZ = 400270 FP 1 /^>ECLAC / FP 10 /^>/ // ID dbigcg-testincfail ER 1 AP seqret CL qangcginc-id:hsfau test.out -auto FI stderr FZ = 122 FP /Error: Unable to read sequence 'qangcginc-id:hsfau'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qangcgall database(s) ############################################# ID dbigcg-allsys-keep DL keep TI 120 AP dbigcg CL -fields "acnum,seqvn,des,keyword,taxon" IN EMBL IN EMBL IN ../../embl IN IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 606 FP /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/ FI entrynam.idx FZ = 1020 FP /\A.{300}AB000095/ FI acnum.hit FZ = 492 FP /\A.{300}\001/ FI acnum.trg FZ = 1068 FP /\A.{308}AB000095/ FI des.hit FZ = 1824 FP /\A.{300}\016/ FI des.trg FZ = 5754 FP /\A.{308}0\000/ FI keyword.hit FZ = 588 FP /\A.{300}\032/ FI keyword.trg FZ = 3264 FP /\A.{308}16P13\000/ FI seqvn.hit FZ = 396 FP /\A.{300}\001/ FI seqvn.trg FZ = 732 FP /\A.{308}AB000095\.1/ FI taxon.hit FZ = 2036 FP /\A.{300}\047/ FI taxon.trg FZ = 3765 FP /\A.{308}AFRICAN CLAWED FROG\000/ // ID dbigcg-allsys-id AP seqret CL qangcgall-id:hsfau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbigcg-allsys-idfirst AP seqret CL qangcgall-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbigcg-allsys-idsecond AP seqret CL qangcgall-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbigcg-allsys-last AP seqret CL qangcgall-id:XLRHODOP test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbigcg-allsys-acc AP seqret CL qangcgall:L07770 test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbigcg-allsys-nextlast AP seqret CL qangcgall-id:XL23808 test.out -auto FI test.out FZ = 4876 FP 1 /^>XL23808 / FP 1 /^>/ // ID dbigcg-allsys-splitfirst AP seqret CL qangcgall-id:CEY39B6 test.out -auto FI test.out FZ = 362911 FP 1 /^>CEY39B6 / FP 1 /^>/ // ID dbigcg-allsys-splitmid AP seqret CL qangcgall-id:PFMAL4P1 test.out -auto FI test.out FZ = 399267 FP 1 /^>PFMAL4P1 / FP 1 /^>/ // ID dbigcg-allsys-splitbefore AP seqret CL qangcgall-id:AC017364 test.out -auto FI test.out FZ = 3801 FP 1 /^>AC017364 / FP 1 /^>/ // ID dbigcg-allsys-splitafter AP seqret CL qangcgall-id:PFMAL4P3 test.out -auto FI test.out FZ = 326444 FP 1 /^>PFMAL4P3 / FP 1 /^>/ // ID dbigcg-allsys-splitend AP seqret CL qangcgall-id:ECUW67 test.out -auto FI test.out FZ = 378731 FP 1 /^>ECUW67 / FP 1 /^>/ // ID dbigcg-allsys-all AP seqret CL qangcgall:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbigcg-allsys-wild AP seqret CL qangcgall:h* test.out -auto FI test.out FZ = 77403 FP 13 /^>H/ FP 13 /^>/ // ID dbigcg-allsys-acnum AP seqret CL qangcgall-acc:X65923 test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbigcg-allsys-acnumall AP seqret CL qangcgall-acc:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbigcg-allsys-acnumwild AP seqret CL qangcgall-acc:x* test.out -auto FI test.out FZ = 18986 FP 11 /^>[A-Z0-9]+ X/ FP 11 /^>/ // ID dbigcg-allsys-sv AP seqret CL qangcgall-sv:D00596.1 test.out -auto FI test.out FZ = 19007 FP 1 /^>HSTS1 / FP 1 /^>/ // ID dbigcg-allsys-svall AP seqret CL qangcgall-sv:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>HSFAU / FP 40 /^>/ // ID dbigcg-allsys-svwild AP seqret CL qangcgall-sv:x* test.out -auto FI test.out FZ = 5045 FP 3 /^>H/ FP 3 /^>/ // ID dbigcg-allsys-des AP seqret CL qangcgall-des:fau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbigcg-allsys-desall AP seqret CL qangcgall-des:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbigcg-allsys-deswild AP seqret CL qangcgall-des:m* test.out -auto FI test.out FZ = 1543930 FP 18 /^>.* [Mm]/ FP 18 /^>/ // ID dbigcg-allsys-key AP seqret CL qangcgall-key:rhodopsin test.out -auto FI test.out FZ = 5087 FP 1 /^>XLRHODOP / FP 3 /^>/ // ID dbigcg-allsys-keyall AP seqret CL qangcgall-key:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbigcg-allsys-keywild AP seqret CL qangcgall-key:m* test.out -auto FI test.out FZ = 9918 FP 1 /^>AB009602/ FP 3 /^>/ // ID dbigcg-allsys-org AP seqret CL qangcgall-org:Mus test.out -auto FI test.out FZ = 473 FP 1 /^>MMAM / FP 1 /^>/ // ID dbigcg-allsys-orgall AP seqret CL qangcgall-org:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbigcg-allsys-orgwild AP seqret CL qangcgall-org:s* test.out -auto FI test.out FZ = 45442 FP 1 /^>MMAM/ FP 5 /^>/ // ID dbigcg-allsys-orgwild2 AP seqret CL qangcgall-org:mus* test.out -auto FI test.out FZ = 4274 FP 1 /^>MMAM/ FP 2 /^>/ // ID dbigcg-allnosys-keep DL keep TI 120 AP dbigcg CL -fields "acnum,seqvn,des,keyword,taxon" -nosystem IN EMBL IN EMBL IN ../../embl IN IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 606 FP /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/ FI entrynam.idx FZ = 1020 FP /\A.{300}AB000095/ FI acnum.hit FZ = 492 FP /\A.{300}\001/ FI acnum.trg FZ = 1068 FP /\A.{308}AB000095/ FI des.hit FZ = 1824 FP /\A.{300}\016/ FI des.trg FZ = 5754 FP /\A.{308}0\000/ FI keyword.hit FZ = 588 FP /\A.{300}\032/ FI keyword.trg FZ = 3264 FP /\A.{308}16P13\000/ FI seqvn.hit FZ = 396 FP /\A.{300}\001/ FI seqvn.trg FZ = 732 FP /\A.{308}AB000095\.1/ FI taxon.hit FZ = 2036 FP /\A.{300}\047/ FI taxon.trg FZ = 3765 FP /\A.{308}AFRICAN CLAWED FROG\000/ // ############################################# # The qapir database(s) ############################################# ID dbigcg-pir-keep DL keep TI 120 AP dbigcg IN PIR IN PIR IN ../../pir IN IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 388 FP /\A.{300}\001\000pir1\.ref pir1\.seq\000/ FI entrynam.idx FZ = 1260 FP /\A.{300}A31558/ FI acnum.hit FZ = 672 FP /\A.{300}\033/ FI acnum.trg FZ = 1392 FP /\A.{308}A00001/ // ID dbigcg-pir-id AP seqret CL qapir-id:cchu test.out -auto FI test.out FZ = 141 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbigcg-pir-idfirst AP seqret CL qapir-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbigcg-pir-idsecond AP seqret CL qapir-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbigcg-pir-last AP seqret CL qapir-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbigcg-pir-acc AP seqret CL qapir:A00001 test.out -auto FI test.out FZ = 141 FP 1 /^>CCHU / FP 1 /^>/ // ID dbigcg-pir-nextlast AP seqret CL qapir-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbigcg-pir-all AP seqret CL qapir:* test.out -auto FI test.out FZ = 10175 FP 1 /^>S11172 / FP 60 /^>/ // ID dbigcg-pir-wild AP seqret CL qapir:c* test.out -auto FI test.out FZ = 7660 FP 49 /^>C/ FP 49 /^>/ // ID dbigcg-pir-testexc AP seqret CL qapirexc-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /\A>S11172 / FP 1 /^>/ // ID dbigcg-pir-testexcall AP seqret CL qapirexc-id:* test.out -auto FI test.out FZ = 2515 FP 1 /^>S11172 / FP 11 /^>/ // ID dbigcg-pir-testexcfail ER 1 AP seqret CL qapirexc-id:cchu test.out -auto FI stderr FZ = 120 FP /Error: Unable to read sequence 'qapirexc-id:cchu'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbigcg-pir-testinc AP seqret CL qapirinc-id:cchu test.out -auto FI test.out FZ = 141 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbigcg-pir-testincall AP seqret CL qapirinc-id:* test.out -auto FI test.out FZ = 7660 FP 1 /^>CCHU / FP 49 /^>/ // ID dbigcg-pir-testincfail ER 1 AP seqret CL qapirinc-id:S11172 test.out -auto FI stderr FZ = 122 FP /Error: Unable to read sequence 'qapirinc-id:S11172'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qapirall database(s) ############################################# # fields seqvn not supported by PIR format data ID dbigcg-pirall-keep DL keep TI 120 AP dbigcg CL -fields "acnum,des,keyword,taxon" IN PIR IN PIR IN ../../pir IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 388 FP /\A.{300}\001\000pir1\.ref pir1\.seq\000/ FI entrynam.idx FZ = 1260 FP /\A.{300}A31558/ FI acnum.hit FZ = 672 FP /\A.{300}\033/ FI acnum.trg FZ = 1392 FP /\A.{308}A00001/ FI des.hit FZ = 1476 FP /\A.{300}\066/ FI des.trg FZ = 3314 FP /\A.{308}0/ FI keyword.hit FZ = 1972 FP /\A.{300}\005/ FI keyword.trg FZ = 828 FP /\A.{308}ACETYLATED AMINO END/ FI taxon.hit FZ = 768 FP /\A.{300}\$/ FI taxon.trg FZ = 4944 FP /\A.{308}AILANTHUS SILKMOTH/ FP /\0ANAS PLATYRHYNCHOS\0/ FP /\0DOMESTIC DUCK\0/ // ID dbigcg-pirall-id AP seqret CL qapirall-id:cchu test.out -auto FI test.out FZ = 141 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbigcg-pirall-idfirst AP seqret CL qapirall-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbigcg-pirall-idsecond AP seqret CL qapirall-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbigcg-pirall-last AP seqret CL qapirall-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbigcg-pirall-acc AP seqret CL qapirall:A00001 test.out -auto FI test.out FZ = 141 FP 1 /^>CCHU / FP 1 /^>/ // ID dbigcg-pirall-nextlast AP seqret CL qapirall-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbigcg-pirall-all AP seqret CL qapirall:* test.out -auto FI test.out FZ = 10175 FP 1 /^>S11172 / FP 60 /^>/ // ID dbigcg-pirall-wild AP seqret CL qapirall:c* test.out -auto FI test.out FZ = 7660 FP 49 /^>C/ FP 49 /^>/ // ID dbigcg-pirall-acnum AP seqret CL qapirall-acc:A04605 test.out -auto FI test.out FZ = 139 FP 1 /\A>CCRT / FP 1 /^>/ // ID dbigcg-pirall-acnumall AP seqret CL qapirall-acc:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCRT / FP 60 /^>/ // ID dbigcg-pirall-acnumwild AP seqret CL qapirall-acc:s* test.out -auto FI test.out FZ = 829 ## CCHO has an S* secondary accession number, rest are primary FP 4 /^>[A-Z0-9]+ S/ FP 5 /^>/ // ID dbigcg-pirall-des AP seqret CL qapirall-des:cytochrome test.out -auto FI test.out FZ = 8516 FP 1 /\A>CCHU / FP 54 /^>/ // ID dbigcg-pirall-desall AP seqret CL qapirall-des:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCHU / FP 60 /^>/ // ID dbigcg-pirall-deswild AP seqret CL qapirall-des:p* test.out -auto FI test.out FZ = 2380 FP 11 /^>.*[ -][Pp]/ FP 11 /^>/ // ID dbigcg-pirall-key AP seqret CL qapirall-key:polymorphism test.out -auto FI test.out FZ = 141 FP 1 /^>CCHU / FP 1 /^>/ // ID dbigcg-pirall-keyall AP seqret CL qapirall-key:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCHU / FP 60 /^>/ // # only entries with keywords ID dbigcg-pirall-keyall2 AP seqret CL qapirall-key:?* test.out -auto FI test.out FZ = 8800 FP 1 /^>CCHU / FP 56 /^>/ // ID dbigcg-pirall-keywild AP seqret CL qapirall-key:m* test.out -auto FI test.out FZ = 8180 FP 1 /^>CCHU / FP 52 /^>/ // ID dbigcg-pirall-org AP seqret CL qapirall-org:'drosophila melanogaster' test.out -auto FI test.out FZ = 180 FP 1 /^>CCFFDM / FP 1 /^>/ // ID dbigcg-pirall-orgall AP seqret CL qapirall-org:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCHU / FP 60 /^>/ // ID dbigcg-pirall-orgwild AP seqret CL qapirall-org:s* test.out -auto FI test.out FZ = 1929 FP 1 /^>CCPG / FP 12 /^>/ // ID dbigcg-pirall-orgwild2 AP seqret CL qapirall-org:mus* test.out -auto FI test.out FZ = 300 FP 1 /^>CCMS / FP 2 /^>/ // ############################################# # The qanxfasta database ############################################# ID dbxfasta-ex-keep DL keep AP dbxfasta IN emrod IN embl IN idacc IN ../../data IN emrod IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /Processing file \S+/test/data/emrod\n/ FI emrod.ent FC = 5 FP 1 /^# Number of files: 1\n/ FP /.*\/test\/data\/emrod\n/ FI emrod.pxac FZ = 115 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 2\n/ FP 1 /^Kwlimit 0\n/ FI emrod.pxid FZ = 115 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 2\n/ FP 1 /^Kwlimit 0\n/ FI emrod.xac FZ = 6144 FP 1 /z46957/ FP 1 /u68037/ FI emrod.xid FZ = 6144 FP 1 /rnops/ FP 1 /rnu68037/ // ID dbxfasta-allsys-keep DL keep AP dbxfasta CL -fields="id,acc,sv,des" IN emrod IN embl IN idacc IN ../../data IN emrod IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /Processing file \S+/test/data/emrod\n/ FI emrod.ent FC = 5 FP 1 /^# Number of files: 1\n/ FP /.*\/test\/data\/emrod\n/ FI emrod.pxac FZ = 115 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 2\n/ FP 1 /^Kwlimit 0\n/ FI emrod.pxde FZ = 120 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 106\n/ FP 1 /^Count 28\n/ FP 1 /^Kwlimit 15\n/ FI emrod.pxid FZ = 115 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 2\n/ FP 1 /^Kwlimit 0\n/ FI emrod.pxsv FZ = 115 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 0\n/ FP 1 /^Kwlimit 0\n/ FI emrod.xac FZ = 6144 FP 1 /z46957/ FP 1 /u68037/ FI emrod.xde FZ = 159744 FP 1 /\0chromosome\0/ FP 2 /\0anti/ FI emrod.xid FZ = 6144 FP 1 /rnops/ FP 1 /rnu68037/ FI emrod.xsv FZ = 2048 FP 2047 /\0/ // ID dbxfasta-idfirst AP seqret CL qanxfasta-id:MMAM test.out -auto FI test.out FZ = 471 FP 1 /^>MMAM / FP 1 /^>/ // ID dbxfasta-idsecond AP seqret CL qanxfasta-id:RNOPS test.out -auto FI test.out FZ = 1565 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbxfasta-last AP seqret CL qanxfasta-id:RNU68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>RNU68037 / FP 1 /^>/ // ID dbxfasta-nextlast AP seqret CL qanxfasta-id:RNOPS test.out -auto FI test.out FZ = 1565 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbxfasta-all AP seqret CL qanxfasta:* test.out -auto FI test.out FZ = 3354 FP 1 /^>RNOPS / FP 3 /^>/ // ID dbxfasta-wild AP seqret CL qanxfasta:r* test.out -auto FI test.out FZ = 2883 FP 1 /^>RNOPS / FP 2 /^>R/ FP 2 /^>/ // ############################################# # The qapfasta database ############################################# ID dbxfasta-swiss-keep DL keep AP dbxfasta IN swnew IN swnew IN idacc IN ../../data IN swnew IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /Processing file \S+/test/data/swnew\n/ FI swnew.ent FC = 5 FP 1 /^# Number of files: 1\n/ FP /.*\/test\/data\/swnew\n/ FI swnew.pxac FZ = 115 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 8\n/ FP 1 /^Kwlimit 0\n/ FI swnew.pxid FZ = 115 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 8\n/ FP 1 /^Kwlimit 0\n/ FI swnew.xac FZ = 6144 FP 2 /\0q90512\0/ FP 1 /\0q90511\0/ FI swnew.xid FZ = 6144 FP 1 /\0co9_fugru\0/ // ID dbxfasta-swiss-idfirst AP seqret CL qapxfasta-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-idsecond AP seqret CL qapxfasta-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-last AP seqret CL qapxfasta-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-nextlast AP seqret CL qapxfasta-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-all AP seqret CL qapxfasta:* test.out -auto FI test.out FZ = 4474 FP 1 /^>E2BB_FUGRU / FP 9 /^>/ // ID dbxfasta-swiss-wild AP seqret CL qapxfasta:n* test.out -auto FI test.out FZ = 516 FP 1 /^>NEUI_FUGRU / FP 2 /^>N/ FP 2 /^>/ // ############################################# # The qawfasta database ############################################# ID dbxfasta-worm-keep DL keep AP dbxfasta IN worm IN swnew IN simple IN ../../data IN wormpep.clone.* IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP 2 /Processing file \S+\/test\/data\/wormpep.clone[.]/ FP 1 /Processing file \S+\/test\/data\/wormpep.clone[.]ZK637\n/ FI worm.ent FC = 6 FP 1 /# Number of files: 2\n/ FP 1 /^\S+\/test\/data\/wormpep.clone.AB\n/ FP 1 /^\S+\/test\/data\/wormpep.clone.ZK637\n/ FI worm.pxac FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 65\n/ FP 1 /^Kwlimit 0\n/ FI worm.pxid FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 65\n/ FP 1 /^Kwlimit 0\n/ FI worm.xid FZ = 8192 FP 1 /\0ah10.1\0/ FI worm.xac FZ = 8192 FP 1 /\0ah10.1\0/ // ID dbxfasta-worm-idfirst AP seqret CL qawxfasta-id:AC3.1 test.out -auto FI test.out FZ = 426 FP 1 /^>AC3[.]1 / FP 1 /^>/ // ID dbxfasta-worm-idsecond AP seqret CL qawxfasta-id:AC3.2 test.out -auto FI test.out FZ = 1057 FP 1 /^>AC3[.]2 / FP 1 /^>/ // ID dbxfasta-worm-last AP seqret CL qawxfasta-id:ZK637.15 test.out -auto FI test.out FZ = 205 FP 1 /^>ZK637[.]15 / FP 1 /^>/ // ID dbxfasta-worm-nextlast AP seqret CL qawxfasta-id:zk637.14 test.out -auto FI test.out FZ = 260 FP 1 /^>ZK637[.]14 / FP 1 /^>/ // ID dbxfasta-worm-all AP seqret CL qawxfasta:* test.out -auto FI test.out FZ = 33816 FP 66 /^>/ // ID dbxfasta-worm-wild AP seqret CL qawxfasta:a* test.out -auto FI test.out FZ = 19764 FP 40 /^>A[^\n]+\n[^>]/ FP 40 /^>/ // ID dbxfasta-worm-wildz AP seqret CL qawxfasta:z* test.out -auto FI test.out FZ = 7264 FP 15 /^>Z[^\n]+\n[^>]/ FP 15 /^>/ // ############################################# # The qanxflat database ############################################# ID dbxflat-ex-keep DL keep AP dbxflat IN embl IN embl IN embl IN rod.dat IN ../../embl IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Processing file .*\/test\/embl\/rod\.dat\n/ FI embl.ent FC = 5 FP /^# Number of files: 1\n/ FP /.*\/test\/embl\/rod\.dat\n/ FI embl.pxac FZ = 115 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 0\n/ FP /^Fill2 0\n/ FP /^Count 2\n/ FP /^Kwlimit 0\n/ FI embl.pxid FZ = 115 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 0\n/ FP /^Fill2 0\n/ FP /^Count 2\n/ FP /^Kwlimit 0\n/ FI embl.xac FZ = 6144 FP /\0l48662\0/ FP /\0l48662\0/ FP /\0z46957\0/ FP /\0u68037\0/ FI embl.xid FZ = 6144 FP /\0mmam\0/ FP /\0rnops\0/ FP /\0rnu68037\0/ // ID dbxflat-id AP seqret CL qanxflat-id:rnops test.out -auto FI test.out FZ = 1567 FP /\A>RNOPS / FP 1 /^>/ // ID dbxflat-idfirst AP seqret CL qanxflat-id:MMAM test.out -auto FI test.out FZ = 473 FP 1 /^>MMAM / FP 1 /^>/ // ID dbxflat-idsecond AP seqret CL qanxflat-id:RNOPS test.out -auto FI test.out FZ = 1567 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbxflat-last AP seqret CL qanxflat-id:RNU68037 test.out -auto FI test.out FZ = 1320 FP 1 /^>RNU68037 / FP 1 /^>/ // ID dbxflat-nextlast AP seqret CL qanxflat-id:RNOPS test.out -auto FI test.out FZ = 1567 FP 1 /^>RNOPS / FP 1 /^>/ // ID dbxflat-all AP seqret CC Fails to fetch all entries in emboss access method CL qanxflat:* test.out -auto FI test.out FZ = 3360 FP 1 /^>RNOPS / FP 3 /^>/ // ID dbxflat-wild AP seqret CL qanxflat:r* test.out -auto FI test.out FZ = 2887 FP 1 /^>RNOPS / FP 2 /^>/ // ############################################# # The qanxflatall database ############################################# ID dbxflat-all-keep DL keep AP dbxflat CL -fields="id,acc,sv,des,key,org" IN embl IN embl IN embl IN IN ../../embl IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 10 FP /^Processing file .*\/test\/embl\/rod\.dat\n/ FP 10 /^Processing file .*\/test\/embl\/[a-z0-9]+\.dat\n/ FI embl.ent FC = 14 FP /^# Number of files: 10\n/ FP /.*\/test\/embl\/rod\.dat\n/ FP 10 /.*\/test\/embl\/[a-z0-9]+\.dat\n/ FI embl.pxac FZ = 116 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 0\n/ FP /^Fill2 0\n/ FP /^Count 87\n/ FP /^Kwlimit 0\n/ FI embl.pxde FZ = 121 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 71\n/ FP /^Fill2 106\n/ FP /^Count 383\n/ FP /^Kwlimit 15\n/ FI embl.pxid FZ = 116 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 0\n/ FP /^Fill2 0\n/ FP /^Count 43\n/ FP /^Kwlimit 0\n/ FI embl.pxkw FZ = 120 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 71\n/ FP /^Fill2 106\n/ FP /^Count 93\n/ FP /^Kwlimit 15\n/ FI embl.pxsv FZ = 116 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 0\n/ FP /^Fill2 0\n/ FP /^Count 43\n/ FP /^Kwlimit 0\n/ FI embl.pxtx FZ = 121 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 71\n/ FP /^Fill2 106\n/ FP /^Count 531\n/ FP /^Kwlimit 15\n/ FI embl.xac FZ = 8192 FP /\0l48662\0/ FP /\0l48662\0/ FP /\0z46957\0/ FP /\0u68037\0/ FI embl.xde FZ = 1437696 FP 2 /\0activator\0/ FI embl.xid FZ = 6144 FP /\0mmam\0/ FP /\0rnops\0/ FP /\0rnu68037\0/ FI embl.xkw FZ = 483328 FP 2 /\0elongation fact\0/ FI embl.xsv FZ = 6144 FP /\0h45989\.1\0/ FI embl.xtx FZ = 698368 FP 1 /\0homo sapiens\0/ // ID dbxflatall-id AP seqret CL qanxflatall-id:rnops test.out -auto FI test.out FZ = 1567 FP /\A>RNOPS / FP 1 />/ // ID dbxflatall-idfirst AP seqret CL qanxflatall-id:MMAM test.out -auto FI test.out FZ = 473 FP 1 />MMAM / FP 1 />/ // ID dbxflatall-idsecond AP seqret CL qanxflatall-id:RNOPS test.out -auto FI test.out FZ = 1567 FP 1 />RNOPS / FP 1 />/ // ID dbxflatall-last AP seqret CL qanxflatall-id:RNU68037 test.out -auto FI test.out FZ = 1320 FP 1 />RNU68037 / FP 1 />/ // ID dbxflatall-nextlast AP seqret CL qanxflatall-id:RNOPS test.out -auto FI test.out FZ = 1567 FP 1 />RNOPS / FP 1 />/ // ID dbxflatall-all AP seqret CC Fails to fetch all entries in emboss access method CL qanxflatall:* test.out -auto FI test.out FZ = 540075 FP 1 />RNOPS / FP 44 />/ // ID dbxflatall-wild AP seqret CL qanxflatall:r* test.out -auto FI test.out FZ = 2887 FP 1 />RNOPS / FP 2 />/ // ID dbxflatall-keywild AP seqret CL qanxflatall-key:a* test.out -auto FI test.out FZ = 89088 FP 1 />HSHBB / FP 7 />/ // ############################################# # The qapxflat database ############################################# ID dbxflat-swiss-keep DL keep AP dbxflat IN swnew IN swnew IN IN IN ../../swnew IN IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /Processing file .*\/test\/swnew\/[a-z_]+\.dat\n/ FP 3 /^Processing file / FI swnew.ent FC = 7 FP /# Number of files: 3\n/ FP /.*\/test\/swnew\/[a-z_]+\.dat\n/ FI swnew.xid FZ = 6144 FP /\0co9_fugru\0/ FI swnew.xac FZ = 6144 FP /\0p53450\0/ FI swnew.pxac FZ = 115 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 0\n/ FP /^Fill2 0\n/ FP /^Count 4\n/ FP /^Kwlimit 0\n/ FI swnew.pxid FZ = 115 FP /^Order 71\n/ FP /^Fill 47\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 0\n/ FP /^Fill2 0\n/ FP /^Count 4\n/ FP /^Kwlimit 0\n/ // ID dbxflat-swiss-idfirst AP seqret CL qapxflat-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-idsecond AP seqret CL qapxflat-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-last AP seqret CL qapxflat-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-nextlast AP seqret CL qapxflat-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-all AP seqret CC Fails to fetch all entries in emboss access method CL qapxflat:* test.out -auto FI test.out FZ = 2413 FP 1 /^>ODO2_FUGRU / FP 5 /^>/ // ID dbxflat-swiss-wild AP seqret CL qapxflat:o* test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-testexc AP seqret CL qapxflatexc-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-testexcall AP seqret CL qapxflatexc-id:* test.out -auto FI test.out FZ = 1978 FP 1 /^>CO9_FUGRU / FP 4 /^>/ // ID dbxflat-swiss-testexcfail ER 1 AP seqret CC exclude not yet implemented for access method emboss CL qapxflatexc-id:FOS_FUGRU test.out -auto FI stderr FZ = 128 FP /Error: Unable to read sequence 'qapxflatexc-id:FOS_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbxflat-swiss-testinc AP seqret CL qapxflatinc-id:FOS_FUGRU test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-testincall AP seqret CL qapxflatinc-id:* test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU / FP 1 /^>/ // ID dbxflat-swiss-testincfail ER 1 AP seqret CC include not yet implemented for access method emboss CL qapxflatinc-id:CO9_FUGRU test.out -auto FI stderr FZ = 128 FP /Error: Unable to read sequence 'qapxflatinc-id:CO9_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qanxgcg database(s) ############################################# ID dbxgcg-ex-keep DL keep TI 120 AP dbxgcg IN embl IN embl IN embl IN ../../embl IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 9 FP 9 /^Processing .*\/test\/embl\/eem_[a-z1-9]+\.seq\n/ FI embl.ent FC = 13 FP 1 /^Dual filename database\n/ FP 1 /^# Number of files: 9\n/ FP 9 /\/test\/embl\/eem_[a-z1-9]+\.ref\n/ FI embl.pxac FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 47\n/ FP 1 /^Kwlimit 0\n/ FI embl.pxid FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 39\n/ FP 1 /^Kwlimit 0\n/ FI embl.xac FZ = 6144 FP 1 /\0ab000095\0/ FI embl.xid FZ = 6144 FP 1 /\0hsfau\0/ // ID dbxgcg-id AP seqret CL qanxgcg-id:hsfau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbxgcg-idfirst AP seqret CL qanxgcg-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbxgcg-idsecond AP seqret CL qanxgcg-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbxgcg-last AP seqret CL qanxgcg-id:XLRHODOP test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbxgcg-acc AP seqret CL qanxgcg:L07770 test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbxgcg-nextlast AP seqret CL qanxgcg-id:XL23808 test.out -auto FI test.out FZ = 4876 FP 1 /^>XL23808 / FP 1 /^>/ // ID dbxgcg-splitfirst AP seqret CL qanxgcg-id:CEY39B6 test.out -auto FI test.out FZ = 362911 FP 1 /^>CEY39B6 / FP 1 /^>/ // ID dbxgcg-splitmid AP seqret CL qanxgcg-id:PFMAL4P1 test.out -auto FI test.out FZ = 399267 FP 1 /^>PFMAL4P1 / FP 1 /^>/ // ID dbxgcg-splitbefore AP seqret CL qanxgcg-id:AC017364 test.out -auto FI test.out FZ = 3801 FP 1 /^>AC017364 / FP 1 /^>/ // ID dbxgcg-splitafter AP seqret CL qanxgcg-id:PFMAL4P3 test.out -auto FI test.out FZ = 326444 FP 1 /^>PFMAL4P3 / FP 1 /^>/ // ID dbxgcg-splitend AP seqret CL qanxgcg-id:ECUW67 test.out -auto FI test.out FZ = 378731 FP 1 /^>ECUW67 / FP 1 /^>/ // ID dbxgcg-all AP seqret CL qanxgcg:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbxgcg-wild AP seqret CL qanxgcg:h* test.out -auto FI test.out FZ = 77403 FP 13 /^>H/ FP 13 /^>/ // ID dbxgcg-testexc AP seqret CL qanxgcgexc-id:hsfau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbxgcg-testexcall AP seqret CL qanxgcgexc-id:* test.out -auto FI test.out FZ = 1744803 FP 1 /^>HSFAU / FP 30 /^>/ // ID dbxgcg-testexcfail ER 1 AP seqret CL qanxgcgexc-id:eclac test.out -auto FI stderr FZ = 123 FP /Error: Unable to read sequence 'qanxgcgexc-id:eclac'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbxgcg-testinc AP seqret CL qanxgcginc-id:eclac test.out -auto FI test.out FZ = 7676 FP 1 /\A>ECLAC / FP 1 /^>/ // ID dbxgcg-testincall AP seqret CL qanxgcginc-id:* test.out -auto FI test.out FZ = 400270 FP 1 /^>ECLAC / FP 10 /^>/ // ID dbxgcg-testincfail ER 1 AP seqret CL qanxgcginc-id:hsfau test.out -auto FI stderr FZ = 123 FP /Error: Unable to read sequence 'qanxgcginc-id:hsfau'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qangcgall database(s) ############################################# ID dbxgcg-allsys-keep DL keep TI 120 AP dbxgcg CL -fields "id,acc,sv,des,key,org" IN embl IN embl IN embl IN ../../embl IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI stdout FC = 9 FP 9 /^Processing .*\/test\/embl\/eem_[a-z1-9]+\.seq\n/ FI embl.ent FC = 13 FP 1 /^Dual filename database\n/ FP 1 /^# Number of files: 9\n/ FP 9 /\/test\/embl\/eem_[a-z1-9]+\.ref\n/ FI embl.pxac FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 47\n/ FP 1 /^Kwlimit 0\n/ FI embl.pxde FZ = 121 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 106\n/ FP 1 /^Count 381\n/ FP 1 /^Kwlimit 15\n/ FI embl.pxid FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 39\n/ FP 1 /^Kwlimit 0\n/ FI embl.pxkw FZ = 120 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 106\n/ FP 1 /^Count 72\n/ FP 1 /^Kwlimit 15\n/ FI embl.pxsv FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 23\n/ FP 1 /^Kwlimit 0\n/ FI embl.pxtx FZ = 121 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 106\n/ FP 1 /^Count 434\n/ FP 1 /^Kwlimit 15\n/ FI embl.xac FZ = 6144 FP 1 /\0ab000095\0/ FI embl.xde FZ = 1257472 FP 1 /\0fau\0/ FI embl.xid FZ = 6144 FP 1 /\0hsfau\0/ FI embl.xkw FZ = 358400 FP 1 /\0rhodopsin\0/ FI embl.xsv FZ = 6144 FP 1 /\0ab000095.1\0/ FI embl.xtx FZ = 616448 FP 1 /\0mus\0/ // ID dbxgcg-allsys-id AP seqret CL qanxgcgall-id:hsfau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbxgcg-allsys-idfirst AP seqret CL qanxgcgall-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbxgcg-allsys-idsecond AP seqret CL qanxgcgall-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbxgcg-allsys-last AP seqret CL qanxgcgall-id:XLRHODOP test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbxgcg-allsys-acc AP seqret CL qanxgcgall:L07770 test.out -auto FI test.out FZ = 1777 FP 1 /^>XLRHODOP / FP 1 /^>/ // ID dbxgcg-allsys-nextlast AP seqret CL qanxgcgall-id:XL23808 test.out -auto FI test.out FZ = 4876 FP 1 /^>XL23808 / FP 1 /^>/ // ID dbxgcg-allsys-splitfirst AP seqret CL qanxgcgall-id:CEY39B6 test.out -auto FI test.out FZ = 362911 FP 1 /^>CEY39B6 / FP 1 /^>/ // ID dbxgcg-allsys-splitmid AP seqret CL qanxgcgall-id:PFMAL4P1 test.out -auto FI test.out FZ = 399267 FP 1 /^>PFMAL4P1 / FP 1 /^>/ // ID dbxgcg-allsys-splitbefore AP seqret CL qanxgcgall-id:AC017364 test.out -auto FI test.out FZ = 3801 FP 1 /^>AC017364 / FP 1 /^>/ // ID dbxgcg-allsys-splitafter AP seqret CL qanxgcgall-id:PFMAL4P3 test.out -auto FI test.out FZ = 326444 FP 1 /^>PFMAL4P3 / FP 1 /^>/ // ID dbxgcg-allsys-splitend AP seqret CL qanxgcgall-id:ECUW67 test.out -auto FI test.out FZ = 378731 FP 1 /^>ECUW67 / FP 1 /^>/ // ID dbxgcg-allsys-all AP seqret CL qanxgcgall:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbxgcg-allsys-wild AP seqret CL qanxgcgall:h* test.out -auto FI test.out FZ = 77403 FP 13 /^>H/ FP 13 /^>/ // ID dbxgcg-allsys-acnum AP seqret CL qanxgcgall-acc:X65923 test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbxgcg-allsys-acnumall AP seqret CL qanxgcgall-acc:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbxgcg-allsys-acnumwild AP seqret CL qanxgcgall-acc:x* test.out -auto FI test.out FZ = 18986 FP 11 /^>[A-Z0-9]+ X/ FP 11 /^>/ // ID dbxgcg-allsys-sv AP seqret CL qanxgcgall-sv:D00596.1 test.out -auto FI test.out FZ = 19007 FP 1 /^>HSTS1 / FP 1 /^>/ // ID dbxgcg-allsys-svall AP seqret CL qanxgcgall-sv:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>HSFAU / FP 40 /^>/ // ID dbxgcg-allsys-svwild AP seqret CL qanxgcgall-sv:x* test.out -auto FI test.out FZ = 5045 FP 3 /^>H/ FP 3 /^>/ // ID dbxgcg-allsys-svwild2 AP seqret CL qanxgcgall-sv:D00596* test.out -auto FI test.out FZ = 19007 FP 1 /^>H/ FP 1 /^>/ // ID dbxgcg-allsys-des AP seqret CL qanxgcgall-des:fau test.out -auto FI test.out FZ = 560 FP 1 /\A>HSFAU / FP 1 /^>/ // ID dbxgcg-allsys-desall AP seqret CL qanxgcgall-des:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbxgcg-allsys-deswild AP seqret CL qanxgcgall-des:m* test.out -auto FI test.out FZ = 1543930 FP 18 /^>.* [Mm]/ FP 18 /^>/ // ID dbxgcg-allsys-key AP seqret CL qanxgcgall-key:rhodopsin test.out -auto FI test.out FZ = 5087 FP 1 /^>XLRHODOP / FP 3 /^>/ // ID dbxgcg-allsys-keyall AP seqret CL qanxgcgall-key:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbxgcg-allsys-keywild AP seqret CL qanxgcgall-key:m* test.out -auto FI test.out FZ = 9918 FP 1 /^>AB009602/ FP 3 /^>/ // ID dbxgcg-allsys-org AP seqret CL qanxgcgall-org:Mus test.out -auto FI test.out FZ = 473 FP 1 /^>MMAM / FP 1 /^>/ // ID dbxgcg-allsys-orgall AP seqret CL qanxgcgall-org:* test.out -auto FI test.out FZ = 2145073 FP 1 /^>XL23808 / FP 40 /^>/ // ID dbxgcg-allsys-orgwild AP seqret CL qanxgcgall-org:s* test.out -auto FI test.out FZ = 45442 FP 1 /^>MMAM/ FP 5 /^>/ // ID dbxgcg-allsys-orgwild2 AP seqret CL qanxgcgall-org:mus* test.out -auto FI test.out FZ = 4274 FP 1 /^>MMAM/ FP 2 /^>/ // ############################################# # The qaxpir database(s) ############################################# ID dbxgcg-pir-keep DL keep TI 120 AP dbxgcg IN pir IN pir IN pir IN ../../pir IN IN FI stderr FC = 12 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP 4 /^Processing file \S+\/test\/pir\/pir[1-4]\.seq\n/ FI pir.ent FC = 8 FP 1 /^# Number of files: 4\n/ FP 1 /^Dual filename database\n/ FP 4 /^\S+\/test\/pir\/pir[1-4]\.seq \S+\/test\/pir\/pir[1-4]\.ref\n/ FI pir.pxac FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 92\n/ FP 1 /^Kwlimit 0\n/ FI pir.pxid FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 59\n/ FP 1 /^Kwlimit 0\n/ FI pir.xac FZ = 10240 FP 1 /\0a00011\0/ FP 2 /\0a04607\0/ FI pir.xid FZ = 6144 FP 1 /\0ccms\0/ FP 2 /\0cchu\0/ // ID dbxgcg-pir-id AP seqret CL qaxpir-id:cchu test.out -auto FI test.out FZ = 141 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbxgcg-pir-idfirst AP seqret CL qaxpir-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbxgcg-pir-idsecond AP seqret CL qaxpir-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbxgcg-pir-last AP seqret CL qaxpir-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbxgcg-pir-acc AP seqret CL qaxpir:A00001 test.out -auto FI test.out FZ = 141 FP 1 /^>CCHU / FP 1 /^>/ // ID dbxxgcg-pir-nextlast AP seqret CL qaxpir-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbxgcg-pir-all AP seqret CL qaxpir:* test.out -auto FI test.out FZ = 10175 FP 1 /^>S11172 / FP 60 /^>/ // ID dbxgcg-pir-wild AP seqret CL qaxpir:c* test.out -auto FI test.out FZ = 7660 FP 49 /^>C/ FP 49 /^>/ // ID dbxgcg-pir-testexc AP seqret CL qaxpirexc-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /\A>S11172 / FP 1 /^>/ // ID dbxgcg-pir-testexcfail ER 1 AP seqret CL qaxpirexc-id:cchu test.out -auto FI stderr FZ = 121 FP /Error: Unable to read sequence 'qaxpirexc-id:cchu'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbxgcg-pir-testinc AP seqret CL qaxpirinc-id:cchu test.out -auto FI test.out FZ = 141 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbxgcg-pir-testincfail ER 1 AP seqret CL qaxpirinc-id:S11172 test.out -auto FI stderr FZ = 123 FP /Error: Unable to read sequence 'qaxpirinc-id:S11172'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qapirall database(s) ############################################# # fields seqvn not supported by PIR format data ID dbxgcg-pirall-keep DL keep TI 120 AP dbxgcg CL -fields "id,acc,des,key,org" IN pir IN pir IN pir IN ../../pir IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP 4 /^Processing file \S+\/test\/pir\/pir[1-4]\.seq\n/ FI pir.ent FC = 8 FP 1 /^# Number of files: 4\n/ FP 1 /^Dual filename database\n/ FP 4 /^\S+\/test\/pir\/pir[1-4]\.seq \S+\/test\/pir\/pir[1-4]\.ref\n/ FI pir.pxac FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 92\n/ FP 1 /^Kwlimit 0\n/ FI pir.pxde FZ = 121 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 106\n/ FP 1 /^Count 294\n/ FP 1 /^Kwlimit 15\n/ FI pir.pxid FZ = 116 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 0\n/ FP 1 /^Fill2 0\n/ FP 1 /^Count 59\n/ FP 1 /^Kwlimit 0\n/ FI pir.pxkw FZ = 121 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 106\n/ FP 1 /^Count 418\n/ FP 1 /^Kwlimit 15\n/ FI pir.pxtx FZ = 121 FP 1 /^Order 71\n/ FP 1 /^Fill 47\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 106\n/ FP 1 /^Count 117\n/ FP 1 /^Kwlimit 15\n/ FI pir.xac FZ = 10240 FP 1 /\0a00011\0/ FP 2 /\0a04607\0/ FI pir.xde FZ = 851968 FP 1 /\0fragments\0/ FP 2 /\0fragment/ FI pir.xid FZ = 6144 FP 1 /\0ccms\0/ FP 2 /\0cchu\0/ FI pir.xkw FZ = 104448 FP 1 /\0heme\0/ FI pir.xtx FZ = 673792 FP 2 /\0anas platyrhynchos\0/ FP 1 /\0domestic duck\0/ FP 1 /\0equus quagga\0/ // ID dbxgcg-pirall-id AP seqret CL qaxpirall-id:cchu test.out -auto FI test.out FZ = 141 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbxgcg-pirall-idfirst AP seqret CL qaxpirall-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbxgcg-pirall-idsecond AP seqret CL qaxpirall-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbxgcg-pirall-last AP seqret CL qaxpirall-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbxgcg-pirall-acc AP seqret CL qaxpirall:A00001 test.out -auto FI test.out FZ = 141 FP 1 /^>CCHU / FP 1 /^>/ // ID dbxgcg-pirall-nextlast AP seqret CL qaxpirall-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbxgcg-pirall-all AP seqret CL qaxpirall:* test.out -auto FI test.out FZ = 10175 FP 1 /^>S11172 / FP 60 /^>/ // ID dbxgcg-pirall-wild AP seqret CL qaxpirall:c* test.out -auto FI test.out FZ = 7660 FP 49 /^>C/ FP 49 /^>/ // ID dbxgcg-pirall-acnum AP seqret CL qaxpirall-acc:A04605 test.out -auto FI test.out FZ = 139 FP 1 /\A>CCRT / FP 1 /^>/ // ID dbxgcg-pirall-acnumall AP seqret CL qaxpirall-acc:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCRT / FP 60 /^>/ // ID dbxgcg-pirall-acnumwild AP seqret CL qaxpirall-acc:s* test.out -auto FI test.out FZ = 829 ## CCHO has an S* secondary accession number, rest are primary FP 4 /^>[A-Z0-9]+ S/ FP 5 /^>/ // ID dbxgcg-pirall-des AP seqret CL qaxpirall-des:cytochrome test.out -auto FI test.out FZ = 8516 FP 1 /^>CCHU / FP 54 /^>/ // ID dbxgcg-pirall-desall AP seqret CL qaxpirall-des:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCHU / FP 60 /^>/ // ID dbxgcg-pirall-deswild AP seqret CL qaxpirall-des:p* test.out -auto FI test.out FZ = 2380 FP 11 /^>.*[ -][Pp]/ FP 11 /^>/ // ID dbxgcg-pirall-key AP seqret CL qaxpirall-key:polymorphism test.out -auto FI test.out FZ = 141 FP 1 /^>CCHU / FP 1 /^>/ // ID dbxgcg-pirall-keyall AP seqret CL qaxpirall-key:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCHU / FP 60 /^>/ // # only entries with keywords ID dbxgcg-pirall-keyall2 AP seqret CL qaxpirall-key:?* test.out -auto FI test.out FZ = 8800 FP 1 /^>CCHU / FP 56 /^>/ // ID dbxgcg-pirall-keywild AP seqret CL qaxpirall-key:m* test.out -auto FI test.out FZ = 8180 FP 1 /^>CCHU / FP 52 /^>/ // ID dbxgcg-pirall-org AP seqret CL qaxpirall-org:'drosophila melanogaster' test.out -auto FI test.out FZ = 180 FP 1 /^>CCFFDM / FP 1 /^>/ // ID dbxgcg-pirall-orgall AP seqret CL qaxpirall-org:* test.out -auto FI test.out FZ = 10175 FP 1 /^>CCHU / FP 60 /^>/ // ID dbxgcg-pirall-orgwild AP seqret CL qaxpirall-org:s* test.out -auto FI test.out FZ = 1929 FP 1 /^>CCPG / FP 12 /^>/ // ID dbxgcg-pirall-orgwild2 AP seqret CL qaxpirall-org:mus* test.out -auto FI test.out FZ = 300 FP 1 /^>CCMS / FP 2 /^>/ // ################################################################## # end of database access tests ################################################################## ID degapseq-ex AP degapseq CL ../../data/dnagap.fasta nogaps.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI nogaps.seq FZ = 138 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID descseq-ex UC Set the name of a sequence to "myclone23" AP descseq CL -seq ../../data/dna.text -out clone23.seq -name "myclone23" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI clone23.seq FZ = 113 FP /^>myclone23\n/ // ID descseq-ex2 UC Set the description of a sequence to "This is my clone number 244" AP descseq CL -seq ../../data/dna.text -out xy24.seq -desc "This is my clone number 244" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI xy24.seq FZ = 142 FP /EMBOSS_001 This is my clone number 244\n/ // ID descseq-ex3 UC Append some text to the description of a sequence AP descseq CL -seq ../../data/dna.text -out est4.seq -desc " (submitted)" -append FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI est4.seq FZ = 127 FP /EMBOSS_001 \(submitted\)\n/ // ID diffseq-ex AP diffseq ## Takes about 3 minutes on original test ## some systems may need longer. ## Or we could go for a shorter example ... TI 300 CL tembl:ap000504 tembl:af129756 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ap000504.diffseq FP /^# AP000504 overlap starts at 1\n/ FP /^# AF129756 overlap starts at 6036\n/ FP /^AP000504 2655-2658 Length: 4\nSequence: tgtg\n/ FI AF129756.diffgff FZ = 11823 FP /^AF129756\tdiffseq\tconflict\t10945\t10962\t1\.000\t.*; note "Insertion of 18 bases in AF129756" ; replace ""\n/ FI AP000504.diffgff FZ = 11774 FP /^AP000504\tdiffseq\tconflict\t847\t847\t1\.000\t.*; note "SNP in AF129756" ; replace "t"\n/ // ID digest-ex AP digest IN tsw:opsd_human IN IN FI stderr FC = 11 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI opsd_human.digest FP /^ 246 248 346\.378 K E AEK\s*\n/ FP /yields 14 fragments/ FC = 34 // ID distmat-ex AP distmat CC Example file missing test/data/pax.align CC No example in the documentation CL ../../data/pax.align IN 2 IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax.distmat FP / Kimura / FP /^\s+0[.]00\s+20[.]37\s+PX8A_HUMAN 9\n/ FC = 17 // ID dotmatcher-ex AP dotmatcher CL tsw:hba_human tsw:hbb_human -graph cps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dotmatcher.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 22 FP /^Created dotmatcher.ps\n/ // ID dotmatcher-data AP dotmatcher CL tsw:hba_human tsw:hbb_human -graph data FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /Created dotmatcher1.dat\n/ FI dotmatcher1.dat FC = 30 FP /^Text2 x1 73.000000 y1 163.5[0-9]+ colour 0 size 1.000000 Dotmatcher: HBA_HUMAN vs HBB_HUMAN\n/ // ID dotmatcher-stretchdata AP dotmatcher CL tsw:hba_human tsw:hbb_human -stretch -xygraph data FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /Created dotmatcher1.dat\n/ FI dotmatcher1.dat FC = 27 FP /^##Title Dotmatcher: HBA_HUMAN vs HBB_HUMAN\n/ FP /^##XminA 1.000000 XmaxA 141.000000 YminA 1.000000 YmaxA 146.000000\n/ FP /^##Xmin 1.000000 Xmax 141.000000 Ymin 1.000000 Ymax 146.000000\n/ FP /^##ScaleXmin 1.000000 ScaleXmax 141.000000 ScaleYmin 1.000000 ScaleYmax 146.000000\n/ FP /^##Maintitle \(windowsize = 10, threshold = 23.00 [0-9\/]+\)\n/ FP /^Line x1 108.000000 y1 113.000000 x2 127.000000 y2 132.000000 colour 0\n/ FP /^##GraphObjects\n/ FP /^##Number 0\n/ // ID dotmatcher-stretch AP dotmatcher CL tsw:hba_human tsw:hbb_human -xygraph ps -stretch IN FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 22 FP /^Created dotmatcher.ps\n/ FI dotmatcher.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID dotpath-ex AP dotpath ## ## timeout 60 seconds on original test system ## TI 400 CL tembl:AF129756 tembl:AP000504 -word 20 -graph cps -overlaps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created dotpath.ps\n/ FI dotpath.ps FZ > 16600 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID dotpath-data AP dotpath ## ## timeout 60 seconds on original test system ## TI 400 CL tembl:AF129756 tembl:AP000504 -word 20 -graph data FI dotpath1.dat FP /^Line x1 10963.000000 y1 4915.000000 x2 10999.000000 y2 4951.000000 colour 0\n/ FC = 146 FI stdout FC = 1 FP /^Created dotpath1.dat\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-ex AP dottup CL tembl:eclac tembl:eclaci -wordsize=6 -gtitle="eclaci vs eclac" -graph cps FI stdout FZ = 18 FP /^Created dottup.ps\n/ FI dottup.ps FZ > 66990 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-data AP dottup CL tembl:eclac tembl:eclaci -wordsize=6 -gtitle="eclaci vs eclac" CL -graph data IN FI stdout FC = 1 FP /^Created dottup1.dat\n/ FI dottup1.dat FC = 2283 FP /^Line x1 5287.000000 y1 624.000000 x2 5298.000000 y2 635.000000 colour 0\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-stretchdata AP dottup CL tembl:eclac tembl:eclaci -wordsize=6 -gtitle="eclaci vs eclac" CL -stretch -xygraph data IN FI stdout FC = 1 FP /^Created dottup1.dat\n/ FI dottup1.dat FC = 2265 FP /^Line x1 5510.000000 y1 195.000000 x2 5521.000000 y2 206.000000 colour 0\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-stretch AP dottup CL tembl:eclac tembl:eclaci -wordsize=6 -gtitle="eclaci vs eclac" -xygraph ps CL -stretch IN FI stdout FZ = 18 FP /^Created dottup.ps\n/ FI dottup.ps FZ > 66990 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dreg-ex AP dreg IN tembl:paamir IN ggtacc IN FI paamir.dreg FZ = 482 FP / 1 6 ggtacc\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID einverted-ex AP einverted ## ## timeout more than 60 seconds ## or we may need a quicker example ## TI 500 CL tembl:hsts1 IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsts1.inv FP /Score 236: 108/130 \( 83%\) matches, 0 gaps/ // ID embossdata-ex UC Display the directories searched for EMBOSS data files: AP embossdata IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /Exists\n/ // ID embossdata-ex2 UC Display the names of data files in all of the possible data directories: UC This is run on a small test system and so the results will probably be different when you run this. AP embossdata CL -showall IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^DIRECTORY: .*data\/?\n/ FP /^DIRECTORY: .*data\/CODONS\/?\n/ FP /^\s*EBLOSUM62\s*\n/ FP /^\s*Eyeast.cut\s*\n/ // ID embossdata-exfile UC Display the directories which contain a particular EMBOSS data file: AP embossdata CL EPAM60 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^File \.\/EPAM60/ FP /^File \.embossdata\/EPAM60/ // ID embossdata-exfetch UC Make a copy of an EMBOSS data file in the current directory: AP embossdata CL -fetch Epepcoil.dat FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^File '.*data\/Epepcoil.dat' has been copied successfully\.\n/ FI Epepcoil.dat FZ = 1445 FP /\A# Input data for PEPCOIL *\n/ // ID embossversion-ex AP embossversion FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^[123].\d+(\.\d+)?\n/ // ID emowse-ex AP emowse IN tsw:* IN ../../data/test.mowse IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 100k_rat.emowse FZ = 8246 FP /^1 100K_RAT/ FP /1 : 100K_RAT\s+1\.277e\+06 100368\.6 0\.750/ // ID emma-ex RQ clustalw AP emma IN ../../data/globins.fasta IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## ## stdout is written by clustalw, invoked by emma ## ## exact output file contents depend on the clustalw version ## this is for clustalw 1.82, built from ## ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.82.UNIX.tar.gz ## file size 606683 date 'Feb 6 2001' ## FI stdout FC > 50 FP /^Sequences \(1:2\) Aligned. Score: 83\n/ FP /^Alignment Score 4164\n/ FP /^GCG-Alignment file created +\S+\Z/ FI hbb_human.aln FZ = 1262 FP /^--------VHLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST\n/ FI hbb_human.dnd FZ = 186 FP /^HBB_HUMAN:0.08080,\nHBB_HORSE:0\.08359\)\n/ // ID entret-ex AP entret CL tembl:hsfau IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.entret FZ = 2868 FP /^FT CDS 57\.\.458\n/ FP /^\/\/\Z/ // ID entret-inauto-acedb AP entret CL -auto ../../data/dna.acedb test.out FI test.out FZ = 117 FC = 4 FP /DNA : "ACEDB"\n/ FP /GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT/ // ID entret-in-acedb AP entret CL -auto ../../data/dna.acedb -sf acedb test.out FI test.out FZ = 117 FC = 4 FP /DNA : "ACEDB"\n/ FP /GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT/ // ID entret-inauto-codata AP entret CL -auto ../../data/dna.codata test.out FI test.out FC = 10 FP /^ENTRY CODATA *\n/ FP /^ 91 G T A C G T A C G T\n/ // ID entret-in-codata AP entret CL -auto ../../data/dna.codata -sf codata test.out FI test.out FZ = 423 FC = 10 FP /^ENTRY CODATA *\n/ FP /^ 91 G T A C G T A C G T\n/ // ID entret-inauto-embl AP entret CL -auto ../../data/dna.embl test.out FI test.out FZ = 487 FC = 18 FP /^ID EMBL standard; DNA; UNC; 100 BP.\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt +100\n/ // ID entret-in-experiment AP entret CL -auto ../../data/xb63c7.s1.exp -sf experiment test.out FI test.out FZ = 2317 FC = 51 FP /^ID xb63c7\.s1\n/ FP /^ TAATTTTCAA AAG-CCA-G\n/ FP /^SR 440\n/ // ID entret-inauto-experiment AP entret CL -auto ../../data/xb63c7.s1.exp test.out FI test.out FZ = 2317 FC = 51 FP /^ID xb63c7\.s1\n/ FP /^ TAATTTTCAA AAG-CCA-G\n/ FP /^SR 440\n/ // ID entret-in-embl AP entret CL -auto ../../data/dna.embl -sf embl test.out FI test.out FZ = 487 FC = 18 FP /^ID EMBL standard; DNA; UNC; 100 BP.\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt +100\n/ // ID entret-inauto-fasta AP entret CL -auto ../../data/dna.fasta test.out FI test.out FZ = 143 FC = 4 FP /^>FASTA F10002 FASTA FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID entret-in-fasta AP entret CL -auto ../../data/dna.fasta -sf fasta test.out FI test.out FZ = 143 FC = 4 FP /^>FASTA F10002 FASTA FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID entret-inauto-gcg AP entret CL -auto ../../data/dna.gcg test.out FI test.out FZ = 362 FC = 14 FP /^GCG Length: 100 Type: N Check: 6856 ..\n/ FP /^ 1 ACGTAC\gnl\|N10002\|NCBI NCBI FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID entret-in-ncbi AP entret CL -auto ../../data/dna.ncbi -sf ncbi test.out FI test.out FZ = 145 FC = 4 FP /^>gnl\|N10002\|NCBI NCBI FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID entret-inauto-nbrf AP entret CL -auto ../../data/prot.nbrf test.out FI test.out FZ = 132 FC = 6 FP /^>P1;pir\n/ FP /^ ABCDEFGHIK LMNPQRSTVW XYZACGTU.-\n/ // ID entret-in-nbrf AP entret CL -auto ../../data/prot.nbrf -sf nbrf test.out FI test.out FZ = 132 FC = 6 FP /^>P1;pir\n/ FP /^ ABCDEFGHIK LMNPQRSTVW XYZACGTU.-\n/ // ID entret-inauto-raw AP entret CL -auto ../../data/dna.text test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-in-raw AP entret CL -auto ../../data/dna.text -sf raw test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-inauto-staden AP entret CL -auto ../../data/dna.staden test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-in-staden AP entret CL -auto ../../data/dna.staden -sf staden test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-inauto-strider AP entret CL -auto ../../data/dna.strider test.out FI test.out FZ = 168 FC = 6 FP /^; DNA sequence STRIDER, 100 bases\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-in-strider AP entret CL -auto ../../data/dna.strider -sf strider test.out FI test.out FZ = 168 FC = 6 FP /^; DNA sequence STRIDER, 100 bases\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-inauto-text AP entret CL -auto ../../data/dna.text test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-in-text AP entret CL -auto ../../data/dna.text -sf text test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID entret-inauto-abi AP entret CC Fails ... ABI reading functions use raw file pointer not the buffer CL -auto ../../data/abiview.abi test.out FI test.out FZ = 0 FI stderr FP /Warning: Unable to read text from binary ABI file ..\/..\/data\/abiview.abi/ FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID entret-inauto-selex AP entret CL -auto ../../data/test.selex test.out FI test.out FZ = 610 FC = 20 FP /^#=ID r17\n/ FP /^lig2 AUGGAUGCGCACC AUCA GGGCGUAUCUAU\n/ // ID entret-in-selex AP entret CL -auto ../../data/test.selex -sf selex test.out FI test.out FZ = 610 FC = 20 FP /^#=ID r17\n/ FP /^lig2 AUGGAUGCGCACC AUCA GGGCGUAUCUAU\n/ // ID entret-inmultiauto-acedb AP entret CL -auto ../../data/dna.m-acedb test.out FI test.out FZ = 420 FC = 15 FP /^DNA : "ACEDBM1"\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID entret-inmulti-acedb AP entret CL -auto ../../data/dna.m-acedb -sf acedb test.out FI test.out FZ = 420 FC = 15 FP /^DNA : "ACEDBM1"\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID entret-inmultiauto-codata AP entret CL -auto ../../data/dna.m-codata test.out FI test.out FZ = 1416 FC = 30 FP /^ENTRY CODATAM1 +\n/ FP /^ 91 G T A C G T A C G T A C G T A C G T A C G T A C G T A C G T\n/ // ID entret-inmulti-codata AP entret CL -auto ../../data/dna.m-codata -sf codata test.out FI test.out FZ = 1416 FC = 30 FP /^ENTRY CODATAM1 +\n/ FP /^ 91 G T A C G T A C G T A C G T A C G T A C G T A C G T A C G T\n/ // ID entret-inmultiauto-embl AP entret CL -auto ../../data/dna.m-embl test.out FI test.out FZ = 945 FC = 21 FP 3 /^ID/ FP /^ +CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT +120\n/ // ID entret-inmulti-embl AP entret CL -auto ../../data/dna.m-embl -sf embl test.out FI test.out FZ = 945 FC = 21 FP 3 /^ID/ FP /^ +CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT +120\n/ // ID entret-inmultiauto-fasta AP entret CL -auto ../../data/dna.m-fasta test.out FI test.out FZ = 516 FC = 12 FP 3 /^>/ FP /^CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA\n/ // ID entret-inmulti-fasta AP entret CL -auto ../../data/dna.m-fasta -sf fasta test.out FI test.out FZ = 516 FC = 12 FP 3 /^>/ FP /^CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA\n/ // ID entret-inmultiauto-msf AP entret CL -auto ../../data/dna.msf test.out FI test.out FZ = 820 FC = 22 FP 3 /^ Name: MSF/ FP /^ MSFM3 ACGTACGTAC GTACGTACGT\n/ // ID entret-inmulti-msf AP entret CL -auto ../../data/dna.msf -sf msf test.out FI test.out FZ = 820 FC = 22 FP 3 /^ Name: MSF/ FP /^ MSFM3 ACGTACGTAC GTACGTACGT\n/ // ID entret-inmultiauto-msf8 AP entret CL -auto ../../data/dna.msf8 test.out FI test.out FZ = 1084 FC = 30 FP 3 /^ Name: fastam/ FP /^fastam3 TACGTACGTA CGTACGTACG T\n/ // ID entret-inmulti-msf8 AP entret CL -auto ../../data/dna.msf8 -sf msf test.out FI test.out FZ = 1084 FC = 30 FP 3 /^ Name: fastam/ FP /^fastam3 TACGTACGTA CGTACGTACG T\n/ // ID entret-inmultiauto-ncbi AP entret CL -auto ../../data/dna.m-ncbi test.out FI test.out FZ = 594 FC = 12 FP 3 /^>/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID entret-inmulti-ncbi AP entret CL -auto ../../data/dna.m-ncbi -sf ncbi test.out FI test.out FZ = 594 FC = 12 FP 3 /^>/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID entret-inmultiauto-phylip AP entret CL -auto ../../data/dna.phylip test.out FI test.out FZ = 495 FC = 12 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID entret-inmulti-phylip AP entret CL -auto ../../data/dna.phylip -sf phylip test.out FI test.out FZ = 495 FC = 12 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID entret-inmultiauto-phylipnon AP entret CL -auto ../../data/dna.phylip3 test.out FI test.out FZ = 492 FC = 10 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID entret-inmulti-phylipnon AP entret CL -auto ../../data/dna.phylip3 -sf phylip test.out FI test.out FZ = 492 FC = 10 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID entret-inmultiauto-strider AP entret CL -auto ../../data/dna.m-strider test.out FI test.out FZ = 648 FC = 21 FP 3 /^; DNA sequence STRIDERM/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID entret-inmulti-strider AP entret CL -auto ../../data/dna.m-strider -sf strider test.out FI test.out FZ = 648 FC = 21 FP 3 /^; DNA sequence STRIDERM/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID entret-inauto-nonewline AP entret CL -auto ../../data/dna.nonewline test.out FI test.out FZ = 51 FC = 2 FP /^>\n/ FP /^aaaaccccggggttttaaaaccccggggttttaaccggttshshshsh$/ // ID entret-inauto-empty AP entret CL -auto stdin test.out ER 1 FI stderr FZ = 109 FP /Error: Unable to read sequence 'stdin'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID epestfind-ex AP epestfind CL -graph cps -invalid IN ../../data/exu2_drops.embl IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created epestfind.ps\n/ FI exu2_drops.epestfind FZ = 3194 FP /238 KMVYEMALQLIESESTESPESFESPESSESSEAEVK 273/ FI epestfind.ps FZ = 26891 FP /^%%Title: PLplot Graph\n/ // ID eprimer3-ex RQ primer3 AP eprimer3 CL tembl:hsfau1 hsfau.eprimer3 -explain FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.eprimer3 FZ = 1427 FP /^\n/ FP /^# considered 16422\n/ FP /^# GC content failed 156\n/ FP /^# ok 2960\n/ FP /^# considered 16330\n/ FP /^# ok 2902\n/ FP /^# considered 2652\n/ FP /^# unacceptable product size 2444\n/ FP /^# ok 186\n/ FP /^ 1 PRODUCT SIZE: 202\n/ FP /^ FORWARD PRIMER 801 20 59\.72 60\.00 CCCAGGAGCTACACACCTTC\n/ FP /^ REVERSE PRIMER 983 20 59\.81 55\.00 GGAGCACGACTTGATCTTCC\n/ FP 5 /PRODUCT SIZE: +[0-9]+/ // ID equicktandem-ex UC The input sequence is the human herpesvirus tandem repeat. AP equicktandem CL -noorigfile IN tembl:hhtetra IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hhtetra.qtan FZ = 532 FP /^ +191 935 339 6 124\n/ // ID est2genome-ex TI 200 AP est2genome IN tembl:hs989235 IN tembl:hsnfg9 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hs989235.est2genome FZ = 3050 FP /Note .* forward est and forward genome, .* imply REVERSED GENE/ FP /^Exon 163 91\.8 25685 25874 HSNFG9 1 193 HS989235/ // ID est2genome-pax TI 200 AP est2genome IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-align TI 200 AP est2genome CL -align IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 8086 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99.2 1380 1510 HSA1280 428 558 pax6/ FP /^HSA1280 9567 ttgaggccctggagaaaggtgat.....ttcagagtttgagagaacccat 10116\n/ FP /^ [|]+>>>>> 515 >>>>>[|]+\n/ FP /^ pax6 1082 ttgaggccctggagaaag...............agtttgagagaacccat 1116\n/ // ID est2genome-align-linear TI 200 AP est2genome CL -align -space 2 IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 8086 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99.2 1380 1510 HSA1280 428 558 pax6/ FP /^HSA1280 9567 ttgaggccctggagaaaggtgat.....ttcagagtttgagagaacccat 10116\n/ FP /^ [|]+>>>>> 515 >>>>>[|]+\n/ FP /^ pax6 1082 ttgaggccctggagaaag...............agtttgagagaacccat 1116\n/ // ID est2genome-align-best TI 200 AP est2genome CL -align -best IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 8086 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-both TI 200 AP est2genome CL -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-both2 TI 200 AP est2genome CL -sreverse -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2104 FP /Note .* forward est and forward genome, .* imply REVERSED GENE/ FP /^Exon 129 99.2 20744 20874 HSA1280 1141 1271 pax6/ CC Note the nosplice version of this test does not have "REVERSED GENE" CC This is only because with no splice consensus penalty the same score CC is found in both directions and the forward gene is the one reported // ID est2genome-mode-forward TI 200 AP est2genome CL -mode forward IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2050 FP /Note requested forward est and forward genome/ FP /^Exon 129 99.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-reverse TI 200 AP est2genome CL -mode reverse -srev1 IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2051 FP /Note requested reversed est and forward genome/ FP /^Exon 129 99.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-reverse2 TI 200 AP est2genome CL -mode reverse IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 47 FP /Note requested reversed est and forward genome/ FP 0 /^Exon/ // ID est2genome-nosplice-both TI 200 AP est2genome CL -nosplice -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 124 99.2 1380 1505 HSA1280 428 553 pax6/ // ID est2genome-nosplice-both2 TI 200 AP est2genome CL -sreverse -nosplice -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 132 99.3 20741 20874 HSA1280 1138 1271 pax6/ CC Note the mode version of this test has "imply REVERSED GENE" CC This is only because with no splice consensus penalty the same score CC is found in both directions and the forward gene is the one reported // ID est2genome-nosplice-forward TI 200 AP est2genome CL -nosplice -mode forward IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2050 FP /Note requested forward est and forward genome/ FP /^Exon 124 99.2 1380 1505 HSA1280 428 553 pax6/ // ID est2genome-nosplice-reverse TI 200 AP est2genome CL -nosplice -mode reverse -srev1 IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2051 FP /Note requested reversed est and forward genome/ FP /^Exon 124 99.2 1380 1505 HSA1280 428 553 pax6/ // ID est2genome-nosplice-reverse2 TI 200 AP est2genome CL -nosplice -mode reverse IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 47 FP /Note requested reversed est and forward genome/ FP 0 /^Exon/ // ID etandem-ex UC The input sequence is the human herpesvirus tandem repeat. AP etandem CL -noorigfile IN tembl:hhtetra IN 6 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hhtetra.tan FZ = 834 FC = 29 FP /^# HitCount: 5\n/ FP /^ 793 936 120 6 24 93.8 acccta \n/ FP /^ 793 936 120 6 24 93.8 acccta \n/ FP /^ 432 485 38 6 9 90.7 ccctaa \n/ FP /^ 494 529 26 6 6 94.4 ccctaa \n/ FP /^ 568 597 24 6 5 100.0 aaccct \n/ // ID extractfeat-ex UC To write out the exons of a sequence: AP extractfeat CL tembl:hsfau1 -type exon stdout FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 743 FP 5 /^>HSFAU1_/ FP /^>HSFAU1_951_1095 \[exon\] H\.sapiens fau 1 gene\n/ FP /^gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag\n/ // ID extractfeat-ex2 UC To write out the exons with 10 extra bases at the start and end so that you can inspect the splice sites: AP extractfeat CL tembl:hsfau1 -type exon -before 10 -after 10 stdout FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 844 FP 5 /^>HSFAU1_/ FP /^>HSFAU1_951_1095 \[exon\] H\.sapiens fau 1 gene\n/ FP /^cccactacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagact\n/ FP /^cctaaggtgagtgaga\n/ // ID extractfeat-ex3 UC To write out the 10 bases around the start of all 'exon' features in the tembl database: AP extractfeat CL tembl:* -type exon -before 5 -after -5 stdout FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 14856 FP 5 /^>HSFAU1_/ FP 138 /^>/ FP /^>HSFAU1_951_1095 \[exon\] H\.sapiens fau 1 gene\n/ // ID extractfeat-ex4 UC To extract the CDS region with the exons joined into one sequence: AP extractfeat CL tembl:hsfau1 -type CDS -join stdout FI stderr FC = 1 FI stdout FZ = 453 FP /^>HSFAU1_782_1912 \[CDS\] H.sapiens fau 1 gene\n/ // # The example has phosphorylation, we only have features that say # PHOSPHORYLATION (BY RK) (BY SIMILARITY). ID extractfeat-ex5 UC To write out the 7 residues around all phosphorylated residues in the tsw database: AP extractfeat CL tsw:* -type mod_res -value phosphorylation* -before 3 -after -4 stdout FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 97 FP 2 /^>/ FP 2 /\[mod_res\]/ FP /^>OPSD_HUMAN_343_343 \[mod_res\] RHODOPSIN\.\n/ FP /^TETSQVA\n/ FP /^>PAXI_HUMAN_118_118 \[mod_res\] PAXILLIN\.\n/ FP /^EHVYSFP\n/ // # use database entry in example ID extractseq-ex UC Extract the region from position 10 to 20: AP extractseq CL tembl:hsfau result.seq -regions '10-20' FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result.seq FZ = 47 FP /^ctcgactccat\n/ // # use database entry in example ID extractseq-ex2 UC Extract the regions 10 to 20, 30 to 45, 533 to 537: AP extractseq CL tembl:hsfau1 result2.seq -regions '10-20 30-45 533-537' FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result2.seq FZ = 71 FP /^tccctctcgatacactcgggacaagttagggc\n/ // # use database entry in example ID extractseq-ex3 UC Extract the regions 782-856, 951-1095, 1557-1612 and 1787-1912: AP extractseq CL tembl:hsfau1 -reg "782..856,951..1095,1557..1612,1787..1912" stdout FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 8 FZ = 447 FP /^atgcagctctttg[^\n]+ccaggaaacg/ FP /^cccacctttggcaagaagaagggccccaatgccaactcttaa\n/ // ID extractseq-ex4 UC Extract the regions 782-856, 951-1095, 1557-1612 and 1787-1912 all to separate output sequences: AP extractseq CL tembl:hsfau1 -reg "782..856,951..1095,1557..1612,1787..1912" stdout -separate FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 13 FZ = 564 FP /^>HSFAU1_782_856/ FP /atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg\ngtcgcccagatcaag/ FP /gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag/ FP /^tcttaa\n/ // ID findkm-ex AP findkm CL -graph cps IN ../../data/enztest.dat IN FI stdout FZ = 18 FP /^Created findkm.ps\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI enztest.findkm FP /^Vmax = 99.70, Km = 4.8946\d+\n/ FI findkm.ps FZ > 30000 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID freak-ex AP freak CL tembl:hsfau IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.freak FP /^24 0.733333\n/ FP /^36 0.600000\n/ FP /^489 0.266667\Z/ FZ = 9827 // ID fuzznuc-ex AP fuzznuc IN tembl:hhtetra IN AAGCTT IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hhtetra.fuzznuc FZ = 571 FP /^# HitCount: 2\n/ FP /^ 1 6 . aagctt\n/ FP /^ 1267 1272 . aagctt\n/ // ID fuzzpro-ex AP fuzzpro IN tsw:* IN [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 100k_rat.fuzzpro FZ = 2380 FP 6 /^# HitCount: 1\n/ FP /^ 53 63 . YVGDEAQSKRG\n/ FP 3 /^ 53 63 . YVGDEAQSKRG\n/ FP 3 /^ 55 65 . YVGDEAQSKRG\n/ // ID fuzztran-ex AP fuzztran CL -opt IN tembl:rnops IN RA IN IN f IN IN FI stderr FC = 31 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rnops.fuzztran FZ = 1135 FP /^# HitCount: 9\n/ FP /^ 919 924 2 . 1 307 308 RA \n/ FP /^ 752 757 2 . 2 251 252 RA \n/ FP /^ 72 77 2 . 3 24 25 RA \n/ FP 6 /^.* 1 +\d+ +\d+ RA +\n/ FP 2 /^.* 2 +\d+ +\d+ RA +\n/ FP 1 /^.* 3 +\d+ +\d+ RA +\n/ // ID feat-embl AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft embl::test.out -auto FI test.out FZ = 78146 ## Internal quotes FP /^FT ""amiE"" gene"\n/ ## Bad features type (CODS) to misc_feature FP /^FT misc_feature 135\.\.1292\n/ ## Case fix for tag /Translation FP /^FT \/translation="MSANSL/ ## Case fix for type Cds FP /^FT CDS 1289\.\.1879\n/ ## Cleanup of extra white space 'positive regulator' FP /\/note="aliphatic amidase regulator, positive regulator of\n/ // ID feat-embl-togff AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft gff::test.out -auto FI test.out FZ = 60761 ## Internal quotes FP /\tCDS\t1289\t1879\t0\.000\t\+\t\.\tSequence "AB036666.58" ; .* of \\"amiE\\" / // ID feat-embl-togb AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft gb::test.out -auto FI test.out FZ = 75357 ## Internal quotes FP /^ ""amiE"" gene"\n/ ## Bad features type (CODS) to misc_feature FP /^ misc_feature 135..1292\n/ ## Case fix for tag /Translation FP /^ \/translation="MSANSL/ ## Case fix for type Cds FP /^ CDS 1289..1879\n/ ## Cleanup of extra white space 'positive regulator' FP /\/note="aliphatic amidase regulator, positive regulator of\n/ // ID feat-genbank-toembl AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.gbft em::test.out -auto FI test.out FZ = 78146 ## Internal quotes FP /^FT ""amiE"" gene"\n/ ## Bad features type (CODS) to misc_feature FP /^FT misc_feature 135..1292\n/ ## Case fix for tag /Translation FP /^FT \/translation="MSANSL/ ## Case fix for type Cds FP /^FT CDS 1289..1879\n/ ## Cleanup of extra white space 'positive regulator' FP /\/note="aliphatic amidase regulator, positive regulator of\n/ // ID feat-pir AP seqret CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir sw::test.out -auto FI test.out FZ = 4842 ## active site two locations with copied annotation (note and comment) FP /^FT ACT_SITE 38 38 Cys, His \(status experimental\)\.\n/ FP /^FT ACT_SITE 90 90 Cys, His \(status experimental\)\.\n/ // ID feat-pir-togff AP seqret CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir gff::test.out -auto FI test.out FZ = 5019 ## active site two locations with copied annotation (note and comment) FP /^OPSD_HUMAN\tPIR\tact_site\t38\t38\t0\.000\t\+\t\.\tSequence "OPSD_HUMAN\.11" ; note "Cys, His" ; comment "status experimental"\n/ FP /^OPSD_HUMAN\tPIR\tact_site\t90\t90\t0\.000\t\+\t\.\tSequence "OPSD_HUMAN.11" ; FeatFlags "0x4"\n/ // ID feat-pir-topir AP seqret CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir pir::test.out -auto FI test.out FZ = 1917 ## active site two locations with copied annotation (note and comment) FP /^F;38,90\/Active site: Cys, His, act_site #status experimental\n/ // ID feat-swiss AP seqret CL -feat tsw:laci_ecoli sw::test.out -auto FI test.out FZ = 1242 FP /^FT DNA_BIND 6 25 H-T-H MOTIF\.\n/ FP /^FT HELIX 32 44\n/ // ID feat-swiss-topir AP seqret CL -feat tsw:laci_ecoli pir::test.out -auto FI test.out FZ = 823 FP /^F;6-25\/Binding site: H-T-H MOTIF, dna_bind\n/ FP /^F;32-44\/Region: helix\n/ // ID feat-swiss-togff AP seqret CL -feat tsw:laci_ecoli gff::test.out -auto FI test.out FZ = 1428 FP /^LACI_ECOLI\tSWISSPROT\tdna_bind\t6\t25\t0\.000\t\+\t\.\tSequence "LACI_ECOLI\.1" ; note "H-T-H MOTIF"\n/ FP /^LACI_ECOLI\tSWISSPROT\thelix\t32\t44\t0.000\t\+\t\.\tSequence "LACI_ECOLI\.9"\n/ // ID garnier-ex AP garnier IN tsw:amic_pseae IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amic_pseae.garnier FP /^# Residue totals: H:111 E: 98 T: 81 C: 94\n/ FP /RADAL\nhelix HHHHHH HHHH H HHHHHH \n/ // ID garnier-range AP garnier CL -sbegin 51 -send 120 IN tsw:amic_pseae IN FI stderr FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FC = 2 FI amic_pseae.garnier FZ = 1144 FP /^# Residue totals: H: 17 E: 21 T: 22 C: 10\n/ FP /RADAL\nhelix HHHHHH HHHH H HHHHHH \n/ FP /^turns T TTT TT TT\n/ // ID garnier-short AP garnier IN asis::GSHQERPL IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI asis.garnier FP /^# Residue totals: H: 0 E: 0 T: 2 C: 6\n/ FP /^turns TT\n/ FP /^ coil CCCCCC \n/ // ID geecee-ex AP geecee CL tembl:hhtetra IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hhtetra.geecee FZ = 42 FP /^HHTETRA 0\.53\n/ // ID getorf-ex AP getorf CL -minsize 300 IN tembl:eclaci IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclaci.orf FZ = 877 FP /^>ECLACI_1 \[735 - 1112\]/ FP /^TGKRAV\n/ FP /^>ECLACI_2 \[1 - 1110\]/ FP /^RQVSRLESGQ\*\n/ FP /^>ECLACI_3 \[465 - 49\]/ // ID helixturnhelix-ex AP helixturnhelix IN tsw:laci_ecoli IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.hth FP /^[(]1[)] Score 2160[.]000 length 22 at residues 4->25\n/ FP /^ Standard_deviations: 6.54\n/ // ID hmoment-ex AP hmoment CL tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hbb_human.hmoment FZ = 1483 FP /^Window: 10 Angle: 100 Max uH: 0\.714\n/ FP /^137\s+0\.299\Z/ // ID iep-ex AP iep CL tsw:laci_ecoli IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.iep FZ = 761 FP /^Isoelectric Point = 6\.8820\n/ FP /^ 7\.00 43\.59 -0\.41\n/ // # change examples to .msf from .seq # ID infoalign-ex AP infoalign CL ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FZ = 761 FP /^msf::.*HBA_HORSE\s+HBA_HORSE\s+141\s+144\s+2\s+3\s+48\s+4\s+89\s+66\.666664\s+0\.190000\s+\n/ // ID infoalign-ex2 UC This example doesn't display the USA of the sequence: AP infoalign CL ../../data/globins.msf -nousa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FZ = 477 FP /^HBA_HORSE\s+141\s+144\s+2\s+3\s+48\s+4\s+89\s+66\.666664\s+0\.190000\s+\n/ // ID infoalign-ex3 UC Display only the name and sequence length of a sequence: AP infoalign CL ../../data/globins.msf -only -name -seqlength IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FZ = 126 FP /^HBA_HORSE\s+141\n/ // ID infoalign-ex4 UC Display only the name, number of gap characters and differences to the consensus sequence: AP infoalign CL ../../data/globins.msf -only -name -gapcount -diffcount IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FZ = 136 FP /^HBA_HORSE\s+3\s+89\n/ // ID infoalign-ex5 UC Display the name and number of gaps within a sequence: AP infoalign CL ../../data/globins.msf -only -name -gaps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FZ = 112 FP /^HBA_HORSE\s+2\n/ // ID infoalign-ex6 UC Display information formatted with HTML: AP infoalign CL ../../data/globins.msf -html IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FZ = 1731 FP /^msf::\.\./\.\./data/globins\.msf:HBA_HORSE<\/td>\n/ FP /^HBA_HORSE<\/td>\n/ // ID infoalign-ex7 UC Use the first sequence as the reference sequence to compare to: AP infoalign CL ../../data/globins.msf -refseq 1 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FZ = 761 FP /^msf::\S+\s+HBA_HORSE\s+141\s+144\s+2\s+3\s+51\s+18\s+72\s+64.583336\s+0\.190000\s+\n/ // ID infoalign-ex8 AP infoalign CL -auto tembl:eclac* -out test.out FI test.out FZ = 764 FP /tembl-id:ECLAC\s+ECLAC\s+7477\s+7477\s+0\s+0\s+65\s+0\s+7412\s+99[.]130[0-9]+\s+1[.]0+\s+E.*/ FP /tembl-id:ECLACZ\s+ECLACZ\s+3078\s+3078\s+0\s+0\s+72\s+0\s+3006\s+97[.]660[0-9]+\s+1[.]0+\s+E.*/ // ID infoalign-ex9 AP infoalign CL -auto tembl:eclacz -out test.out FI test.out FZ = 245 FP /tembl-id:ECLACZ\s+ECLACZ\s+3078\s+3078\s+0\s+0\s+0\s+0\s+3078\s+100[.]0+\s+1[.]0+\s+E.*/ // ID infoseq-ex UC Display information on a sequence: AP infoseq CL tembl:paamir FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 202 FP /^tembl-id:PAAMIR\s+PAAMIR\s+X13776\s+N\s+2167\s+66\.54\s+Pseudomonas/ // ID infoseq-ex2 UC Don't display the USA of a sequence: AP infoseq CL tembl:paamir -nousa FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 168 FP /^PAAMIR\s+X13776\s+N\s+2167\s+66\.54\s+Pseudomonas/ // ID infoseq-ex3 UC Display only the name and length of a sequence: AP infoseq CL tembl:paamir -only -name -length FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^PAAMIR\s+2167\n/ // ID infoseq-ex4 UC Display only the description of a sequence: AP infoseq CL tembl:paamir -only -desc FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 75 FP /^Pseudomonas aeruginosa .* regulation\n/ // ID infoseq-ex5 UC Display the type of a sequence: AP infoseq CL tembl:paamir -only -type FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 2 FP /^N\n/ // ID infoseq-ex6 UC Display information formatted with HTML: AP infoseq CL tembl:paamir -html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 354 FP /^tembl-id:PAAMIRPAAMIRX13776N216766.54 Pseudomonas .* regulation\n/ // ID isochore-ex CC Change to reading tembl:AF129756 - much faster AP isochore CL tembl:AF129756 -graph cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI af129756.iso FZ = 22819 FP /^5000\s+0.476\n/ FI isochore.ps FZ > 100 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 20 FP /^Created isochore.ps\n/ // ID jembossctl-ex CC for jemboss installations CC can only be run through tomcat so simply exits here AP jembossctl CL jctl.file FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // # remove the extra 2 prompts from the example ID lindna-ex AP lindna CL -graph cps IN ../../data/data.linp IN IN FI stdout FZ = 18 FP /^Created lindna.ps\n/ FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI lindna.ps FZ = 14370 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ## Example should be file1 file2 ID listor-ex UC Write the logical OR of two lists: AP listor CL ../../data/file1 ../../data/file2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 115 FC = 4 FP 4 /^fasta::/ FP 3 /file1/ FP 1 /file2/ // ID listor-ex2 UC Write the logical AND of two lists: AP listor CL ../../data/file1 ../../data/file2 -operator and IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 58 FC = 2 FP 2 /^fasta::/ FP 2 /file1/ FP 0 /file2/ // ID listor-ex3 UC Write the logical XOR of two lists: AP listor CL ../../data/file1 ../../data/file2 -operator xor IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 57 FC = 2 FP 2 /^fasta::/ FP 1 /file1/ FP 1 /file2/ // ID listor-ex4 UC Write the logical NOT of two lists: AP listor CL ../../data/file1 ../../data/file2 -operator not IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 28 FC = 1 FP 1 /^fasta::/ FP 1 /file1/ FP 0 /file2/ FP 1 /file1:one/ // ID marscan-ex AP marscan IN tembl:u01317 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hshbb.marscan FZ = 1524 FP /\t2242\t2458\t.*start8bp 2451".*end8bp 2458".*start16bp 2242".*end16bp 2257"\n/ // ID maskfeat-ex UC Mask out a feature whose type is "repeat_region" from position 2331 to 2356: AP maskfeat CL tembl:ab000360 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ab000360.fasta FZ = 2685 FP /^>AB000360 / FP /^NNNNNNNNNNNNNNNNaaagtcacttctttctacccttttcaatgtgctaatgctctttt\n/ // ID maskfeat-ex2 UC Change to lower-case a feature whose type is "repeat_region" from position 2331 to 2356. Note that '-supper' is used to make the whole sequence upper-case before the lower-case masking: AP maskfeat CL tembl:ab000360 -tolower -supper IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ab000360.fasta FZ = 2685 FP /^>AB000360 / FP /^gtgtgtgtgtgtgtgtAAAGTCACTTCTTTCTACCCTTTTCAATGTGCTAATGCTCTTTT\n/ // ID maskseq-ex UC Mask off bases 10 to 12 from a sequence 'prot.fasta' and write to the new sequence file 'prot2.seq': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=10-12 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKXXXPQRSTVWYACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY\n/ // ID maskseq-ex2 UC Mask off bases 20 to 30 from a sequence 'prot.fasta' using the character 'x' and write to the new sequence file 'prot2.seq': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=20-30 -mask=x FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKLMNPQRSTVWxxxxxxxxxxxMNPQRSTVWYACDEFGHIKLMNPQRSTVWY\n/ // ID maskseq-ex3 UC Mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKLMNPQRSTVWXXXXEFGHIKLMNPXXXXXXXXXXXXGHIKLMNPQRSTVWY\n/ FP /^ACDEFGHIKLMNPQRSTVWYACDEFGHXXXMNPQRSTVWY\n/ // ID maskseq-ex4 UC Change to lower-case the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 -tolower FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKLMNPQRSTVWyacdEFGHIKLMNPqrstvwyacdefGHIKLMNPQRSTVWY\n/ FP /^ACDEFGHIKLMNPQRSTVWYACDEFGHiklMNPQRSTVWY\n/ // ID matcher-ex AP matcher CL tsw:hba_human tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.matcher FP /^# Identity: +63\/145 \(43\.4%\)/ FP /^# Score: +264\n/ FP /^HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP\n/ FC = 46 // ID matcher-ex2 UC To find the 10 best alignments: AP matcher CL tsw:hba_human tsw:hbb_human -alt 10 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.matcher FP /^# Identity: +63\/145 \(43\.4%\)/ FP /^# Score: +264\n/ FP /^HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP\n/ FC = 271 // ID megamerger-ex TI 300 AP megamerger CL tembl:ap000504 tembl:af129756 IN IN IN report FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI report FZ = 30354 FP /^AP000504 overlap starts at 1\n/ FP /^AF129756 overlap starts at 6036\n/ ## ## silly example - output is identical to af129756 ## FI ap000504.merged FZ = 187844 FP /^gaattctctccctcccatctgtggctgagattaaagatctgcacctgaagcactgaagaa\n/ FP /^tcctgctcctagaagctaaactctccagacttagtcttctgaattc\n/ // ID merger-ex AP merger IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FZ > 1445 FP /^# Score: 795\.0\n/ FP /^ECLACY +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^ECLACA +1 [-]+gtgaatgaa +9\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID msbar-ex UC This asks for 5 mutations, with point mutations as changes (substitutions), and the codon and block mutations ignored. AP msbar IN tembl:eclac IN 5 IN 4 IN IN IN FI stderr FC = 26 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## ## hard to test - different changes each time FI eclac.fasta FZ = 7678 FP /^>ECLAC J01636/ // ID mwcontam-ex AP mwcontam IN ../../data/mw1.dat,../../data/mw2.dat,../../data/mw3.dat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.mwcontam FZ = 15 FP /^67\.000\n/ FP /^415\.000\n/ // ID mwfilter-ex AP mwfilter IN ../../data/molwts.dat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI molwts.mwfilter FZ = 190 FC = 16 FP /^874\.364756\n/ // ID needle-ex AP needle CL tsw:hba_human tsw:hbb_human IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.needle FZ > 1270 FP /^# Score: 290\.5\n/ FP /HBB_HUMAN +1 +VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDL +48\n/ FP /HBA_HUMAN +49 +S-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRV +93\n/ // ID newcpgreport-ex AP newcpgreport IN tembl:rnu68037 IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rnu68037.newcpgreport FZ = 542 FP /^FT CpG island 104\.\.509\n/ FP /^FT \/size=406\n/ FP /^FT \/Sum C\+G=269\n/ FP /^FT \/Percent CG=66\.26\n/ FP /^FT \/ObsExp=0.81\n/ FP /^FT CpG island 596\.\.924\n/ FP /^FT numislands 2\n/ // ID newcpgseek-ex AP newcpgseek IN tembl:rnu68037 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rnu68037.newcpgseek FZ = 279 FP /^with score \> 17 \n/ FP /^\* 96 1032 630 87 66\.1 0\.65\n/ FP /^ 1072 1100 26 3 62\.1 0\.00\n/ FP /^ 1183 1193 26 2 72\.7 2\.00\n/ // # example to use SWISS format (for protein) ID newseq-ex UC Type in a short sequence to the file 'mycc.pep' in SWISSPROT format: AP newseq IN cytoc IN fragment of cytochrome c IN p IN KKKEERADLIAY IN swiss::mycc.pep FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mycc.pep FZ = 162 FP /^ID cytoc STANDARD; PRT; 12 AA\.\n/ FP /^DE fragment of cytochrome c\n/ FP /^SQ SEQUENCE 12 AA; 1464 MW; 6F142FA88DADC40B CRC64;/ // ID noreturn-ex AP noreturn CL ../../data/abc.dat IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI abc.noreturn FZ = 71 FP /carriage return format\nACDEFGHIKLMNPQRSTVWY\n$/ // ID noreturn-topc AP noreturn CL ../../data/abc.dat -system pc IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI abc.noreturn FZ = 73 FP /carriage return format\r\nACDEFGHIKLMNPQRSTVWY\r\n$/ // ID noreturn-tomac AP noreturn CL ../../data/abc.dat -system mac IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI abc.noreturn FZ = 71 FP /carriage return format\rACDEFGHIKLMNPQRSTVWY\r$/ // # change example to use globins.fasta ID notseq-ex UC In this case the excluded sequences (myg_phyca and lgb2_luplu) are not saved to any file: AP notseq IN ../../data/globins.fasta IN myg_phyca,lgb2_luplu IN mydata.seq FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mydata.seq FZ = 926 FP /^>HBA_HUMAN/ FP /^>HBA_HORSE/ FP /^>HBB_HUMAN/ FP /^>HBB_HORSE/ FP /^>GLB5_PETMA/ FP 0 /^>MYG_PHYCA/ FP 0 /^>LGB2_LUPLU/ // ID notseq-ex2 UC Here is an example where the sequences to be excluded are saved to another file: AP notseq CL -junkout hb.seq IN ../../data/globins.fasta IN hb* IN mydata.seq FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mydata.seq FZ = 581 FP 0 /^>HBA_HUMAN/ FP 0 /^>HBA_HORSE/ FP 0 /^>HBB_HUMAN/ FP 0 /^>HBB_HORSE/ FP /^>GLB5_PETMA/ FP /^>MYG_PHYCA/ FP /^>LGB2_LUPLU/ FI hb.seq FP /^>HBB_HUMAN/ // ID nthseq-ex AP nthseq IN tembl:eclac* IN 2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.fasta FZ = 1942 FP /^>ECLACA X51872.1 Escherichia coli lacA gene/ // ID octanol-ex AP octanol IN tsw:opsd_human IN ps FI stdout FZ = 19 FP /^Created octanol.ps\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI octanol.ps FZ = 17968 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID octanol-nodiff AP octanol CL -nodiff IN tsw:opsd_human IN ps FI stdout FZ = 19 FP /^Created octanol.ps\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI octanol.ps FZ = 13936 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID oddcomp-ex UC To search for entries in swissprot with at least 1 SR AND at least 2 RS: CC test.comp input file missing AP oddcomp IN tsw:* IN ../../data/oddcomp.comp IN IN out.odd FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI out.odd FP /CB1B_FUGRU/ FZ = 175 // ID palindrome-ex AP palindrome IN tembl:hsts1 IN 15 IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsts1.pal FZ = 1383 FP /^Palindromes:\n126 caaaaaaaaaaaaaaaa 142\n/ FP /^217 gtttttttttttttttt 201\n/ FP /^127 aaaaaaaaaaaaaaaagaccgccagggct 155\n/ FP /^204 ttttttttttttttttctggcggtcccga 176\n/ // # change the examples to use these files ID pasteseq-ex UC To insert the sequence 'tsw:flav_nossm' after position 67 in sequence 'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta': AP pasteseq CL tsw:amir_pseae tsw:flav_nossm -pos=67 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir_pseae.fasta FZ = 276 FP /^FQNGHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL\n/ // ID pasteseq-ex2 UC This does the same thing, but the output qualifier is explicitly used: AP pasteseq CL tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amirplus.seq FZ = 276 FP /^FQNGHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL\n/ // ID pasteseq-ex3 UC To insert the sequence 'tsw:flav_nossm' before the start of sequence 'tsw:amir_pseae' use -pos=0: AP pasteseq CL tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amirplus.seq FZ = 276 FP /^DALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVAL\n/ // ID patmatdb-ex AP patmatdb IN tsw:* IN st[ty]s IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 100k_rat.patmatdb FZ = 1285 FP /^# Sequence: HD_FUGRU from: 1 to: 3148\n# HitCount: 1\n/ FP /^Length = 4\n/ FP /^Start = position 1038 of sequence\n/ FP /^End = position 1041 of sequence\n/ FP /^STPASSTTSSAVDP\n/ // # change the example (was an arabidopsis entry) ID patmatmotifs-ex AP patmatmotifs ## split export EMBOSS_DATA=../prosextract-keep/ into two statements PP EMBOSS_DATA=../prosextract-keep/ PP export EMBOSS_DATA CL -full IN tsw:opsd_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI opsd_human.patmatmotifs FP /^# HitCount: 2\n/ FP /^# Motif: OPSIN\n# Count: 1\n/ FP /^Start = position 123 of sequence\n/ FP /^End = position 139 of sequence\n/ FP /^Length = 17\n/ FP /^Motif = G_PROTEIN_RECEP_F1_1\n/ FP /^TLGGEIALWSLVVLAIERYVVVCKPMS\n/ // ID pepcoil-ex AP pepcoil IN tsw:gcn4_yeast IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI gcn4_yeast.pepcoil FZ = 258 FP /^Other structures from 1 to 232 \(232 residues\)\n/ FP /^ Max score: 1\.283 \(probability 0\.21\)\n/ FP /^Prediction starts at 233\n/ FP /^Probable coiled-coil from 233 to 281 \(49 residues\)\n/ FP /^ Max score: 1\.910 \(probability 1\.00\)\n/ OC The SwissProt annotation marks the true leucine zipper motif as from 253 to 274. OC The leucine zipper is a special case of a coiled-coil region. // ID pepinfo-ex AP pepinfo IN tsw:opsd_human IN cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created pepinfo.ps\n/ FI opsd_human.pepinfo FZ = 202670 FP 3 /^\s+4\s+T\s+1\n/ FP 6 /^\s+4\s+T\s+0\n/ FP 3 /^\s+4\s+T\s+0\.000\n/ FI pepinfo.ps FZ = 758243 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 2\n/ // ID pepnet-ex AP pepnet CL -sask IN tsw:gcn4_yeast IN 253 IN 274 IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 18 FP /^Created pepnet.ps\n/ FI pepnet.ps FZ = 12979 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepnet-data AP pepnet CL -sask -graph data ## No -outfile qualifier - fixed filename IN tsw:gcn4_yeast IN 253 IN 274 IN cps FI stdout FC = 1 FP /^Created pepnet1.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pepnet1.dat FC = 104 FP /^Text1 x1 139.599991 y1 93.500000 colour 1 size 0.750000 D\n/ FP /^Rectangle x1 134.499985 y1 85.430000 x2 137.499985 y2 88.430000 colour 9\n/ // ID pepstats-ex AP pepstats IN tsw:laci_ecoli IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.pepstats FZ = 1410 FP /^Molecular weight = 38563\.97/ FP /^Average Residue Weight = 107\.122\s+Charge\s+= 1\.5\s+\n/ FP /^Isoelectric Point = 6\.8820\n/ FP /^A280 Molar Extinction Coefficient = 21620\s+\n/ FP /^A280 Extinction Coefficient 1mg/ml = 0.56\s+\n/ FP /^Improbability of expression in inclusion bodies = 0\.670\n/ FP /^A = Ala\s+44\s+12\.222\s+1\.421\s+\n/ FP /^Tiny\s+\(A\+C\+G\+S\+T\)\s+121\s+33\.611\n/ // ID pepwheel-ex AP pepwheel CL tsw:hbb_human -send 30 IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 20 FP /^Created pepwheel.ps\n/ FI pepwheel.ps FZ = 13599 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwheel-data AP pepwheel CL tsw:hbb_human -send 30 -graph data FI stdout FC = 1 FP /^Created pepwheel1.dat\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pepwheel1.dat FC = 138 FP /^Text1 x1 -?0.000000 y1 0.453300 colour 9 size 1.000000 V\n/ FP /^Rectangle x1 -0.025000 y1 0.431300 x2 0.025000 y2 0.481300 colour 9\n/ // ID pepwindow-ex AP pepwindow CL tsw:hba_human IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created pepwindow.ps\n/ FI pepwindow.ps FZ = 14717 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwindow-local AP pepwindow PP EMBOSS_DATA=../aaindexextract-keep/ PP export EMBOSS_DATA CL tsw:hba_human IN ps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created pepwindow.ps\n/ FI pepwindow.ps FZ = 14647 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwindow-localdata AP pepwindow PP EMBOSS_DATA=../aaindexextract-keep/ PP export EMBOSS_DATA CL tsw:hba_human -datafile chop780101 IN ps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created pepwindow.ps\n/ FI pepwindow.ps FZ = 14249 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwindow-localfail AP pepwindow ER 1 PP EMBOSS_DATA=../aaindexextract-keep/ PP export EMBOSS_DATA CL tsw:hba_human -datafile fail780101 IN ps FI stderr FC = 3 FP /^Error: Unable to open data file 'fail780101' for input\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // # change example to globins.msf (plural) ID pepwindowall-ex AP pepwindowall CL ../../data/globins.msf -gxtitle="Base Number" -gytitle="hydropathy" IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 24 FP /^Created pepwindowall.ps\n/ FI pepwindowall.ps FZ = 22479 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // # change example to use globins.msf ID plotcon-ex AP plotcon CL -sformat msf ../../data/globins.msf -graph cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created plotcon.ps\n/ FI plotcon.ps FZ = 20936 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID plotcon-data AP plotcon CL -sformat msf ../../data/globins.msf -graph data IN FI stdout FC = 1 FP /^Created plotcon1.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI plotcon1.dat FC = 179 FP /^##Points 164\n/ FP /^10.000000\s+0.000744\n/ // ID plotorf-ex AP plotorf IN tembl:paamir IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created plotorf.ps\n/ FI plotorf.ps FZ = 41629 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID plotorf-ex2 UC An example of specifying your own START and STOP codons with a mitochondrial sequence would be: AP plotorf CL -start ATT,ATC,ATA,ATG,GTG -stop TAA,TAG,AGA,AGG IN ../../data/mito.seq IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created plotorf.ps\n/ FI plotorf.ps FZ = 177905 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID polydot-ex AP polydot CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta" CL -graph cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created polydot.ps\n/ FI polydot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID polydot-data AP polydot CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta" CL -graph data IN FI stdout FC = 1 FP /^Created polydot1.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI polydot1.dat FC = 201 FP /^##Screen x1 -163.350006 y1 -163.350006 x2 1690.672485 y2 1252.349976\n/ FP /^Textline x1 -98.010010 y1 73.000000 x2 -98.010010 y2 146.000000 colour 0 size 0.300000 HBB_HUMAN\n/ FP /^Rectangle x1 0.000000 y1 156.000000 x2 146.000000 y2 302.000000 colour 0\n/ FP /^Text1 x1 1121.670044 y1 1056.329956 colour 0 size 0.300000 No. Length Lines Points Sequence\n/ FP /^Text1 x1 1121.670044 y1 1023.659973 colour 0 size 0.300000 1 146 8 248 HBB_HUMAN\n/ // ID polydot-feat AP polydot CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta" CL -graph cps -dumpfeat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created polydot.ps\n/ FI polydot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI globins.gff FP /HBB_HUMAN\s+wordmatch\s+misc_feature\s+88\s+111\s+1.000\s+[+]\s+[.]\s+Sequence "HBB_HUMAN.1" ; note "HBB_HORSE"\n/ // ID preg-ex AP preg IN tsw:*_rat IN IA[QWF]A IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 100k_rat.preg FZ = 485 FP /^ 390 393 IAQA\n/ // ID prettyplot-ex AP prettyplot CL -resbreak=10 -boxcol -consensus -plurality=3 IN ../../data/globins.msf IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 22 FP /^Created prettyplot.ps\n/ FI prettyplot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 3\n/ // ID prettyplot-data AP prettyplot CL -resbreak=10 -boxcol -consensus -plurality=3 CL -graph data IN ../../data/globins.msf FI stdout FC = 2 FP /^Created prettyplot2.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prettyplot1.dat FC = 1252 FP /^Text1 x1 -10.000000 y1 50.200001 colour 0 size 8.000000 LGB2_LUPLU\n/ FP /^Text1 x1 -10.000000 y1 43.599998 colour 0 size 8.000000 Consensus\n/ FP /^Text1 x1 59.000000 y1 53.500000 colour 0 size 8.000000 50\n/ FP /^Text1 x1 4.000000 y1 53.500000 colour 0 size 8.000000 D\n/ FI prettyplot2.dat FC = 130 FP /^Text1 x1 -10.000000 y1 50.200001 colour 0 size 8.000000 LGB2_LUPLU\n/ // ID prettyplot-ex2 AP prettyplot CL ../../data/globins.msf -plurality=3 -docolour IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 22 FP /^Created prettyplot.ps\n/ FI prettyplot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 2\n/ // ID prettyseq-ex AP prettyseq IN tembl:paamir IN 135-1292 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.prettyseq FZ = 8166 FP / 121 AGGAGAGGAAACGGatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180\n/ FP / 1 M G S H Q E R P L I G L L F S E 16\n/ // ID primersearch-ex AP primersearch CL tembl:z52466 IN ../../data/primers IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsa203yc1.primersearch FZ = 405 FP /^Primer name D1S2660\nAmplimer 1\n/ FP /^\tSequence: HSA203YC1 Z52466 \n/ FP /^\tH.sapiens \(D1S2660\) DNA segment containing \(CA\) repeat; clone AFMa203yc1; single read\.\n/ FP /^\tCACACATGCACATGCAC hits forward strand at 27 with 0 mismatches\n/ FP /^\tAGTGACACCAGCAGGG hits reverse strand at \[103\] with 0 mismatches\n/ FP /^\tAmplimer length: 261 bp\n/ // ID primersearch-ex2 UC Here we run the same example but allowing 20% mismatch between the primers and the sequence: AP primersearch CL tembl:z52466 IN ../../data/primers IN 20 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsa203yc1.primersearch FZ = 686 FP /^Amplimer 1\n\tSequence: HSA203YC1 Z52466 \n/ FP /^Amplimer 2\n\tSequence: HSA203YC1 Z52466 \n/ FP /^\tCACACATGCACATGCAC hits forward strand at 49 with 2 mismatches\n/ // ## commit a data/seqs.list file for input ##ID primersearch-ex3 ##UC Here is an example of running with a file containing a list of sequences: ##CC Need the seqs.list input list ##AP primersearch ##CL @../../data/seqs.list ##IN ../../data/primers ##IN ##IN ##FI stderr ##FC = 2 ##FP 0 /Warning: / ##FP 0 /Error: / ##FP 0 /Died: / ##FI hs214yg7.primersearch ##FZ = 0 ##// ID printsextract-keep DL keep PP mkdir ./PRINTS ## split export EMBOSS_DATA=./ into two statements PP EMBOSS_DATA=./ PP export EMBOSS_DATA AP printsextract IN ../../data/prints.test FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI PRINTS // ID profit-ex AP profit ## changed to a matrix file which produces some results ##IN ../../data/globins.prophecy IN ../../data/outfile.prophecy IN tsw:* IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.profit FZ = 122 FP /^HBB_HUMAN/ // ID prophecy-ex AP prophecy IN ../../data/globins.msf IN IN globins IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.prophecy FZ = 13782 FC = 173 FP /^Maximum score\s+496\n/ FP /^Consensus\s+PIVDT.*AAYQG\n/ // ID prophecy-ex2 AP prophecy IN ../../data/globins.msf IN g IN IN globins IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.prophecy ## ## Do not check file size. AIX reports -0.00 in some positions ## so the file can be slightly larger ## FP /^Max_score\s+645\.45\n/ FP /^Consensus\s+PIVDT.*ELGYQG\n/ FP /^0\.15 0\.00 0\.03 0\.03 0\.03 -0\.18 .* 0\.87 0\.87\n/ // # example - use h* to save time ID prophet-ex TI 600 AP prophet IN tsw:h* IN ../../data/globins.gribskov IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hd_fugru.prophet FP /^Score: 170.08\n/ FP /^Consensus +15 +ELSAVDKAWVKAN\.SVAEVGGHALERGLFASEPMTLEFFDTFKYL 58 +\n/ FP /^HBA_HUMAN +1 +VLSPADKTNVKAAWG\.GKVGAHAGEYGAEALERMFLSFPTTKTYF 44 +\n/ // ID prosextract-keep AP prosextract DL keep ## split export EMBOSS_DATA=./ into two statements PP mkdir ./PROSITE PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI PROSITE // ID pscan-ex AP pscan ## split export EMBOSS_DATA=./ into two statements PP EMBOSS_DATA=../printsextract-keep/ PP export EMBOSS_DATA IN tsw:opsd_human IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI opsd_human.pscan FZ = 871 FP /^Fingerprint GPCRRHODOPSN Elements 7\n Accession number PR00237\n/ FP /^ Element 2 Threshold 49% Score 75%\n/ FP /^ Start position 72 Length 22\n/ FP /^ Element 1 Threshold 54% Score 64%\n/ FP /^ Start position 39 Length 25\n/ // ID psiphi-ex AP psiphi CL ../../data/1hmp_a.ccf -chainnumber=1 -startresiduenumber=5 -finishresiduenumber=85 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 1hmp_a.psiphi FZ = 3862 FP / 56 56 0\.0 \-139\.15 162\.01\n/ // ID rebaseextract-keep AP rebaseextract DL keep PP mkdir ./REBASE ## split export EMBOSS_DATA=./ into two statements PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/withrefm IN ../../data/proto FI embossre.equ FZ = 76 FP 1 /BshI HaeIII/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI REBASE // ID recoder-ex AP recoder ## split export EMBOSS_DATA=../rebaseextract-keep/ into two statements PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:hsfau IN EcoRII IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.recoder FZ = 3209 FP 3 / +77 +81 . +EcoRII +CCWGG +78 +P.P +C->[ACGT]\n/ // ID recoder-seqs AP recoder ## split export EMBOSS_DATA=../rebaseextract-keep/ into two statements PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -sshow -tshow IN tembl:hsfau IN EcoRII IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.recoder FZ = 5036 FP 3 / +77 +81 . +EcoRII +CCWGG +78 +P.P +C->[ACGT]\n/ FP /# 61 +AGCTCTTTGT CCGCGCCCAG GAGCTACACA CCTTCGAGGT GACCGGCCAG GAAACGGTCG \n/ // # make bamhi explicit in reply to prompt ID redata-ex AP redata ## split export EMBOSS_DATA=../rebaseextract-keep/ into two statements PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN BamHI IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.redata FP /\ABamHI\n/ FP /^Recognition site is GGATCC leaving sticky ends\n/ FP /^ Cut positions 5':1 3':5\n/ // ID remap-ex UC This example uses only a small region of the input sequence to save space. UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap ## split export EMBOSS_DATA=../rebaseextract-keep/ into two statements PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 IN tembl:eclac IN taqi,bsu6i,acii,bsski IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.remap FZ = 1226 FP /^# Enzymes that cut.*\n(\s+\S+\s+1\s+\S*\n){4}\n/ FP /^# Enzymes that do not cut.*\n\n/ FP /^\s+AciI\s+1\s+\n/ FP /^\s+BssKI\s+1\s+\n/ FP /^\s+Ksp632I\s+1\s+Bsu6I\n/ FP /^\s+TaqI\s+1\s+\n/ // ID remap-ex2 UC This is an example where all enzymes in the REBASE database are used, UC (but only the prototypes of the isoschizomers are reported by default). UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap ## split export EMBOSS_DATA=../rebaseextract-keep/ into two statements PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 IN tembl:eclac IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.remap FZ = 1848 FP /^\s+Hin6I\s+2\s+HinP1I,HspAI\n/ // ID remap-ex3 UC This is an example where all enzymes in the REBASE database are used UC but the -limit qualifier is not set so that all of the enzymes are UC displayed and not just only the prototypes of the isoschizomers. UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap ## split export EMBOSS_DATA=../rebaseextract-keep/ into two statements PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 -nolimit IN tembl:eclac IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.remap FZ = 2057 FP /^\s+TaqI\s+1\s+\n/ // ID remap-ex4 UC This shows the 'flat' format: UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 -flat IN tembl:eclac IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.remap FZ = 2242 FP /^\s+Hin6I\s+2\s+HinP1I,HspAI\n/ // ID restover-ex AP restover ## split export EMBOSS_DATA=../rebaseextract-keep/ into two statements PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:hsfau IN cg IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.restover FZ = 1122 FP /^# Number of hits with any overlap: 54\n/ FP /^\s+11\s+TaqI\s+TCGA\s+11\s+13\s+\n/ // ID restrict-ex AP restrict PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:hsfau IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.restrict FP /^\s+11\s+14\s+TaqI\s+TCGA\s+11\s+13\s+[.]\s+[.]\n/ FP /^\s+125\s+135\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+148\s+143\n/ // ID restrict-ex2 UC This gives the lengths of the restriction fragments produced by UC cutting with all of the specified enzymes. AP restrict CL -fragments PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:hsfau IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.restrict FP /^\s+11\s+14\s+TaqI\s+TCGA\s+11\s+13\s+[.]\s+[.]\n/ FP /^\s+125\s+135\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+148\s+143\n/ FP /^#\s+79/ // ID restrict-ex3 UC This gives the lengths of the restriction fragments created by UC cutting with just one of each of the specified enzymes in turn. AP restrict CL -solofragment PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:hsfau IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.restrict FP /^\s+11\s+14\s+TaqI\s+TCGA\s+11\s+13\s+[.]\s+[.]\n/ FP /^\s+125\s+135\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+148\s+143\n/ FP /^#\s+3\s+13\s+25\s+33\s+37\s+114/ // ID restrict-nonpal UC Tests non-palindromic sites AP restrict PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -enzymes BseYI IN asis:GCTGGGTTTCCCAGC IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI asis.restrict FP /^\s+6\s+1\s+BseYI\s+CCCAGC\s+1\s+5\s+[.]\s+[.]\n/ FP /^\s+10\s+15\s+BseYI\s+\CCCAGC\s+10\s+14\s+[.]\s+[.]\n/ // ID revseq-ex UC To create the reverse complement (reverse sense) of 'tembl:hsfau' in the file 'hsfau.rev': AP revseq CL tembl:hsfau hsfau.rev FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.rev FZ = 562 FP /^gtcccagctaccgcgaagatggagtcgagaaagaggaa\n/ // ID revseq-ex2 UC To create the complement of 'tembl:hsfau' in the file 'hsfau.rev': AP revseq CL tembl:hsfau hsfau.rev -norev FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.rev FZ = 562 FP /^agattattttttcggtgaatcaagtcagtttttttttt\n/ // ID revseq-ex3 UC To create the reverse of 'tembl:hsfau' in the file 'hsfau.rev': AP revseq CL tembl:hsfau hsfau.rev -nocomp FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.rev FZ = 562 FP /^cagggtcgatggcgcttctacctcagctctttctcctt\n/ // ID seealso-ex AP seealso IN matcher FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 6 FP /^seqmatchall/ FP /^supermatcher/ FP /^water/ FP /^wordmatch/ // ID seqmatchall-ex UC Here is an example using an increased word size to avoid accidental matches: AP seqmatchall IN tembl:eclac* IN 15 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.seqmatchall FZ = 1535 FP /^ 1832 ECLAC +[+] +5646..7477 ECLACA +[+] +1..1832\n/ FP /^ 1113 ECLAC +[+] +49..1161 ECLACI +[+] +1..1113\n/ FP /^ 1500 ECLAC +[+] +4305..5804 ECLACY +[+] +1..1500\n/ FP /^ 3078 ECLAC +[+] +1287..4364 ECLACZ +[+] +1..3078\n/ FP /^ 159 ECLACA +[+] +1..159 ECLACY +[+] +1342..1500\n/ FP /^ 60 ECLACY +[+] +1..60 ECLACZ +[+] +3019..3078\n/ // ########################################################################### # first entry in first file ID seqret-dbidfilefirst AP seqret CL -auto tembl:HS989235 test.out FI test.out FP 1 /\A>HS989235 / // # last entry in last file ID seqret-dbidfilelast AP seqret CL -auto tembl-id:XL23808 test.out FI test.out FP 1 /\A>XL23808 / // # last entry in last file ID seqret-dbacfilelast AP seqret CL -auto tembl-acc:U23808 test.out FI test.out FP 1 /\A>XL23808 U23808.1 / // ID seqret-dbacfirst AP seqret CL -auto tembl-acc:AB000095 test.out FI test.out FP 1 /\A>AB000095 AB000095.1 / // ID seqret-dbacnextlast AP seqret CL -auto tembl-acc:Z52466 test.out FI test.out FP 1 /\A>HSA203YC1 Z52466.1 / // ID seqret-dbaclast AP seqret CL -auto tembl-acc:Z69719 test.out FI test.out FP 1 /\A>HSNFG9 Z69719.1 / // ID seqret-inlist-good AP seqret CL -auto @../../data/good.list test.out -osf embl FI test.out FZ = 584 FP 3 /^ID .* AA\.\n/ FP /^SQ SEQUENCE 56 AA; 6466 MW; 48CB2E252357CBF6 CRC64;/ // ID seqret-inlist-bad AP seqret CL -auto @../../data/bad.list test.out -osf embl FI stderr FZ = 112 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /^Error: failed to open filename '\.\.\/\.\.\/data\/alignc\.prot'\n/ FP /^Error: Unable to read sequence '\.\.\/\.\.\/data\/alignc\.prot'\n/ FI test.out FP 3 /^ID .* AA\.\n/ FP /^SQ SEQUENCE 56 AA; 6466 MW; 48CB2E252357CBF6 CRC64;/ // ID seqret-inlist-ugly AP seqret CL -auto @../../data/ugly.list test.out -osf embl FI stderr FZ = 46 FP /^Error: Unable to read sequence 'tembl:eclacj'\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seqret-inlist-uglyfirst AP seqret CL -auto @../../data/uglyfirst.list test.out -osf embl FI stderr FZ = 46 FP /^Error: Unable to read sequence 'tembl:eclacj'\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seqret-inlist-uglylast AP seqret CL -auto @../../data/uglylast.list test.out -osf embl FI stderr FZ = 46 FP /^Error: Unable to read sequence 'tembl:eclacj'\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seqret-inlist-uglyall AP seqret CL -auto @../../data/uglyall.list test.out -osf embl FI stderr FZ = 138 FP /^Error: Unable to read sequence 'tembl:eclacj'\n/ FP /^Error: Unable to read sequence 'tembl:eclack'\n/ FP /^Error: Unable to read sequence 'tembl:eclacl'\n/ FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seqret-inauto-acedb AP seqret CL -auto ../../data/dna.acedb test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-acedb AP seqret CL -auto acedb::../../data/dna.acedb test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-acedb AP seqret CL -auto ../../data/dna.acedb -sf acedb test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-codata AP seqret CL -auto ../../data/dna.codata test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-codata AP seqret CL -auto codata::../../data/dna.codata test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-codata AP seqret CL -auto ../../data/dna.codata -sf codata test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-embl AP seqret CL -auto ../../data/dna.embl test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-embl AP seqret CL -auto embl::../../data/dna.embl test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-embl AP seqret CL -auto ../../data/dna.embl -sf embl test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-experiment AP seqret CL -auto ../../data/xb63c7.s1.exp test.out -osf embl FI test.out FP /^ID .* 439 BP\.\n/ FP /^SQ Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/ // ID seqret-inusa-experiment AP seqret CL -auto experiment::../../data/xb63c7.s1.exp test.out -osf embl FI test.out FP /^ID .* 439 BP\.\n/ FP /^SQ Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/ // ID seqret-in-experiment AP seqret CL -auto ../../data/xb63c7.s1.exp -sf experiment test.out -osf embl FI test.out FP /^ID .* 439 BP\.\n/ FP /^SQ Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/ // ID seqret-inauto-fasta AP seqret CL -auto ../../data/dna.fasta test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-fasta AP seqret CL -auto fasta::../../data/dna.fasta test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-fasta AP seqret CL -auto ../../data/dna.fasta -sf fasta test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-gcg AP seqret CL -auto ../../data/dna.gcg test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-gcg AP seqret CL -auto gcg::../../data/dna.gcg test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-gcg AP seqret CL -auto ../../data/dna.gcg -sf gcg test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-gcg8 AP seqret CL -auto ../../data/dna.gcg8 test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-gcg8 AP seqret CL -auto gcg8::../../data/dna.gcg8 test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-gcg8 AP seqret CL -auto ../../data/dna.gcg8 -sf gcg8 test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-genbank AP seqret CL -auto ../../data/dna.genbank test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-genbank AP seqret CL -auto genbank::../../data/dna.genbank test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-genbank AP seqret CL -auto ../../data/dna.genbank -sf genbank test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-ig ## ## We expect failure - IG is not allowed for automatic detection ## because it can read almost anything as 'valid' ## ER 1 AP seqret CL -auto ../../data/dna.ig test.out -osf embl FI stderr FP /Unable to read sequence .*/dna\.ig/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-inusa-ig AP seqret CL -auto ig::../../data/dna.ig test.out -osf embl FI test.out FP /^ID .* 100 BP/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-ig AP seqret CL -auto ../../data/dna.ig -sf ig test.out -osf embl FI test.out FP /^ID .* 100 BP/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-ncbi AP seqret CL -auto ../../data/dna.ncbi test.out -osf embl FI test.out FP /^ID .* 100 BP/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-ncbi AP seqret CL -auto ncbi::../../data/dna.ncbi test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-ncbi AP seqret CL -auto ../../data/dna.ncbi -sf ncbi test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-nbrf AP seqret CL -auto ../../data/prot.nbrf test.out -osf swiss FI test.out FZ = 246 FP /^ID pir .* 90 AA\.\n/ FP /^DE example pir format\n/ FP /^SQ SEQUENCE 90 AA; 9815 MW; 5B548D9C397EC1FE CRC64;/ // ID seqret-inusa-nbrf AP seqret CL -auto nbrf::../../data/prot.nbrf test.out -osf swiss FI test.out FZ = 246 FP /^ID pir .* 90 AA\.\n/ FP /^DE example pir format\n/ FP /^SQ SEQUENCE 90 AA; 9815 MW; 5B548D9C397EC1FE CRC64;/ // ID seqret-in-nbrf AP seqret CL -auto ../../data/prot.nbrf -sf nbrf test.out -osf swiss FI test.out FZ = 246 FP /^ID pir .* 90 AA\.\n/ FP /^DE example pir format\n/ FP /^SQ SEQUENCE 90 AA; 9815 MW; 5B548D9C397EC1FE CRC64;/ // ID seqret-inauto-raw AP seqret CL -auto ../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-raw AP seqret CL -auto raw::../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-raw AP seqret CL -auto ../../data/dna.text -sf raw test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-staden AP seqret CL -auto ../../data/dna.staden test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-staden AP seqret CL -auto staden::../../data/dna.staden test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-staden AP seqret CL -auto ../../data/dna.staden -sf staden test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-strider AP seqret CL -auto ../../data/dna.strider test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-strider AP seqret CL -auto strider::../../data/dna.strider test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-strider AP seqret CL -auto ../../data/dna.strider -sf strider test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-text AP seqret CL -auto ../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inusa-text AP seqret CL -auto text::../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-text AP seqret CL -auto ../../data/dna.text -sf text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-inauto-abi AP seqret CL -auto ../../data/abiview.abi test.out -osf embl FI test.out FZ = 1246 FP /^ID .* 838 BP\.\n/ FP /^SQ Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/ // ID seqret-inusa-abi AP seqret CL -auto abi::../../data/abiview.abi test.out -osf embl FI test.out FZ = 1246 FP /^ID .* 838 BP\.\n/ FP /^SQ Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/ // ID seqret-in-abi AP seqret CL -auto ../../data/abiview.abi -sf abi test.out -osf embl FI test.out FZ = 1246 FP /^ID .* 838 BP\.\n/ FP /^SQ Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/ // ID seqret-inauto-selex AP seqret CL -auto ../../data/test.selex test.out -osf embl FI test.out FZ = 532 FP 3 /^ID/ FP /^ID lig28.* 31 BP\.\n/ FP /^SQ Sequence 31 BP; 7 A; 7 C; 8 G; 7 T; 2 other;/ // ID seqret-inusa-selex AP seqret CL -auto selex::../../data/test.selex test.out -osf embl FI test.out FZ = 532 FP 3 /^ID/ FP /^ID lig28.* 31 BP\.\n/ FP /^SQ Sequence 31 BP; 7 A; 7 C; 8 G; 7 T; 2 other;/ // ID seqret-in-selex AP seqret CL -auto ../../data/test.selex -sf selex test.out -osf embl FI test.out FZ = 532 FP 3 /^ID/ FP /^ID lig28.* 31 BP\.\n/ FP /^SQ Sequence 31 BP; 7 A; 7 C; 8 G; 7 T; 2 other;/ // ID seqret-inmultiauto-acedb AP seqret CL -auto ../../data/dna.m-acedb test.out -osf embl FI test.out FP 1 /^ID ACEDBM1 .* 120 BP\.\n/ FP 1 /^ID ACEDBM2 .* 120 BP\.\n/ FP 1 /^ID ACEDBM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiusa-acedb AP seqret CL -auto acedb::../../data/dna.m-acedb test.out -osf embl FI test.out FP 1 /^ID ACEDBM1 .* 120 BP\.\n/ FP 1 /^ID ACEDBM2 .* 120 BP\.\n/ FP 1 /^ID ACEDBM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmulti-acedb AP seqret CL -auto ../../data/dna.m-acedb -sf acedb test.out -osf embl FI test.out FP 1 /^ID ACEDBM1 .* 120 BP\.\n/ FP 1 /^ID ACEDBM2 .* 120 BP\.\n/ FP 1 /^ID ACEDBM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiauto-codata AP seqret CL -auto ../../data/dna.m-codata test.out -osf embl FI test.out FP 1 /^ID CODATAM1 .* 120 BP\.\n/ FP 1 /^ID CODATAM2 .* 120 BP\.\n/ FP 1 /^ID CODATAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiusa-codata AP seqret CL -auto codata::../../data/dna.m-codata test.out -osf embl FI test.out FP 1 /^ID CODATAM1 .* 120 BP\.\n/ FP 1 /^ID CODATAM2 .* 120 BP\.\n/ FP 1 /^ID CODATAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmulti-codata AP seqret CL -auto ../../data/dna.m-codata -sf codata test.out -osf embl FI test.out FP 1 /^ID CODATAM1 .* 120 BP\.\n/ FP 1 /^ID CODATAM2 .* 120 BP\.\n/ FP 1 /^ID CODATAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiauto-embl AP seqret CL -auto ../../data/dna.m-embl test.out -osf embl FI test.out FP 1 /^ID FASTAM1 .* 120 BP\.\n/ FP 1 /^ID FASTAM2 .* 120 BP\.\n/ FP 1 /^ID FASTAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiusa-embl AP seqret CL -auto embl::../../data/dna.m-embl test.out -osf embl FI test.out FP 1 /^ID FASTAM1 .* 120 BP\.\n/ FP 1 /^ID FASTAM2 .* 120 BP\.\n/ FP 1 /^ID FASTAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmulti-embl AP seqret CL -auto ../../data/dna.m-embl -sf embl test.out -osf embl FI test.out FP 1 /^ID FASTAM1 .* 120 BP\.\n/ FP 1 /^ID FASTAM2 .* 120 BP\.\n/ FP 1 /^ID FASTAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiauto-fasta AP seqret CL -auto ../../data/dna.m-fasta test.out -osf embl FI test.out FP 1 /^ID FASTAM1 .* 120 BP\.\n/ FP 1 /^ID FASTAM2 .* 120 BP\.\n/ FP 1 /^ID FASTAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiusa-fasta AP seqret CL -auto fasta::../../data/dna.m-fasta test.out -osf embl FI test.out FP 1 /^ID FASTAM1 .* 120 BP\.\n/ FP 1 /^ID FASTAM2 .* 120 BP\.\n/ FP 1 /^ID FASTAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmulti-fasta AP seqret CL -auto ../../data/dna.m-fasta -sf fasta test.out -osf embl FI test.out FP 1 /^ID FASTAM1 .* 120 BP\.\n/ FP 1 /^ID FASTAM2 .* 120 BP\.\n/ FP 1 /^ID FASTAM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiauto-msf AP seqret CL -auto ../../data/dna.msf test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiusa-msf AP seqret CL -auto msf::../../data/dna.msf test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmulti-msf AP seqret CL -auto ../../data/dna.msf -sf msf test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiauto-msf8 AP seqret CL -auto ../../data/dna.msf8 test.out -osf embl FI test.out FP 1 /^ID fastam1 .* 121 BP\.\n/ FP 1 /^ID fastam2 .* 121 BP\.\n/ FP 1 /^ID fastam3 .* 121 BP\.\n/ FP 2 /^SQ Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/ FP 1 /^SQ Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/ // ID seqret-inmultiusa-msf8 AP seqret CL -auto msf::../../data/dna.msf8 test.out -osf embl FI test.out FP 1 /^ID fastam1 [^\n]* 121 BP\.\n/ FP 1 /^ID fastam2 [^\n]* 121 BP\.\n/ FP 1 /^ID fastam3 [^\n]* 121 BP\.\n/ FP 2 /^SQ Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/ FP 1 /^SQ Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/ // ID seqret-inmulti-msf8 AP seqret CL -auto ../../data/dna.msf8 -sf msf test.out -osf embl FI test.out FP 1 /^ID fastam1 .* 121 BP\.\n/ FP 1 /^ID fastam2 .* 121 BP\.\n/ FP 1 /^ID fastam3 .* 121 BP\.\n/ FP 2 /^SQ Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/ FP 1 /^SQ Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/ // ID seqret-inmultiauto-ncbi AP seqret CL -auto ../../data/dna.m-ncbi test.out -osf embl FI test.out FP 1 /^ID N30001 .* 144 BP\.\n/ FP 1 /^ID N30002 .* 144 BP\.\n/ FP 1 /^ID N30003 .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seqret-inmultiusa-ncbi AP seqret CL -auto ncbi::../../data/dna.m-ncbi test.out -osf embl FI test.out FP 1 /^ID N30001 .* 144 BP\.\n/ FP 1 /^ID N30002 .* 144 BP\.\n/ FP 1 /^ID N30003 .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seqret-inmulti-ncbi AP seqret CL -auto ../../data/dna.m-ncbi -sf ncbi test.out -osf embl FI test.out FP 1 /^ID N30001 .* 144 BP\.\n/ FP 1 /^ID N30002 .* 144 BP\.\n/ FP 1 /^ID N30003 .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seqret-inmultiauto-phylip AP seqret CL -auto ../../data/dna.phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiusa-phylip AP seqret CL -auto phylip::../../data/dna.phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmulti-phylip AP seqret CL -auto ../../data/dna.phylip -sf phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiauto-phylipnon AP seqret CL -auto ../../data/dna.phylip3 test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiusa-phylipnon AP seqret CL -auto phylipnon::../../data/dna.phylip3 test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmulti-phylipnon AP seqret CL -auto ../../data/dna.phylip3 -sf phylipnon test.out -osf embl FI test.out FP 1 /^ID MSFM1 .* 120 BP\.\n/ FP 1 /^ID MSFM2 .* 120 BP\.\n/ FP 1 /^ID MSFM3 .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seqret-inmultiauto-strider AP seqret CL -auto ../../data/dna.m-strider test.out -osf embl FI test.out FP 1 /^ID STRIDERM1 .* 144 BP\.\n/ FP 1 /^ID STRIDERM2 .* 144 BP\.\n/ FP 1 /^ID STRIDERM3 .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seqret-inmultiusa-strider AP seqret CL -auto strider::../../data/dna.m-strider test.out -osf embl FI test.out FP 1 /^ID STRIDERM1 .* 144 BP\.\n/ FP 1 /^ID STRIDERM2 .* 144 BP\.\n/ FP 1 /^ID STRIDERM3 .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seqret-inmulti-strider AP seqret CL -auto ../../data/dna.m-strider -sf strider test.out -osf embl FI test.out FP 1 /^ID STRIDERM1 .* 144 BP\.\n/ FP 1 /^ID STRIDERM2 .* 144 BP\.\n/ FP 1 /^ID STRIDERM3 .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seqret-inauto-nonewline AP seqret CL -auto ../../data/dna.nonewline test.out -osf embl FI test.out FP /^ID .* 48 BP\.\n/ FP /^SQ Sequence 48 BP; 10 A; 10 C; 10 G; 10 T; 8 other;/ // ID seqret-inauto-empty AP seqret CL -auto stdin test.out -osf embl ER 1 FI stderr FZ = 109 FP /Error: Unable to read sequence 'stdin'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-in-badformat ## ## bad format name - but still reads (auto) it if it can ## AP seqret CL -auto ../../data/dna.fasta -sf badformat test.out -osf embl FI stderr FP /Unknown input format 'badformat'/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP /^ID .* 100 BP\.\n/ FP /SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-in-badusaformat ## ## bad format name - but still reads (auto) it if it can ## AP seqret CL -auto badformat::../../data/dna.fasta test.out -osf embl FI stderr FP /Unknown input format 'badformat'/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP /^ID .* 100 BP\.\n/ FP /SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seqret-outusa-acedb AP seqret CL -auto ../../data/dna.embl acedb::test.out FI test.out FZ = 116 FP /^DNA : "EMBL"\n/ // ID seqret-out-acedb AP seqret CL -auto ../../data/dna.embl test.out -osf acedb FI test.out FZ = 116 FP /^DNA : "EMBL"\n/ // ID seqret-outusa-asn1 AP seqret CL -auto ../../data/dna.embl asn1::test.out FI test.out FZ = 291 FP /repr raw, mol dna, length 100, topology linear,/ FP /id \{ local id 1 \},/ // ID seqret-out-asn1 AP seqret CL -auto ../../data/dna.embl test.out -osf asn1 FI test.out FZ = 291 FP /repr raw, mol dna, length 100, topology linear,/ FP /id \{ local id 1 \},/ // ID seqret-outusa-codata AP seqret CL -auto ../../data/dna.embl codata::test.out FI test.out FZ = 419 FP /^ 61 a c g t a c g t a c g t a c g t a c g t a c g t a c g t a c\n/ FP /^ENTRY EMBL/ FP /^TITLE EMBL FORMAT DNA SEQUENCE, 100 bases/ FP /^ACCESSION E10002/ FP /^\/\/\/\n/ // ID seqret-out-codata AP seqret CL -auto ../../data/dna.embl test.out -osf codata FI test.out FZ = 419 FP /^ 61 a c g t a c g t a c g t a c g t a c g t a c g t a c g t a c\n/ FP /^ENTRY EMBL/ FP /^TITLE EMBL FORMAT DNA SEQUENCE, 100 bases/ FP /^ACCESSION E10002/ FP /^\/\/\/\n/ // ID seqret-outusa-debug AP seqret CL -auto ../../data/dna.embl debug::test.out FI test.out FZ = 863 FP /^ Name: 'EMBL'\n/ FP /^ Accession: 'E10002'\n/ FP /^ SeqVersion: 'E10002.34'\n/ FP /^ GenInfo Id: ''\n/ FP /^ Description: 'EMBL FORMAT DNA SEQUENCE'\n/ FP /^ Keywordlist: \(2\)\n/ FP /^ 'DNA binding protein'\n/ FP /^ 'repressor'\n/ FP /^ Taxonomy: 'Escherichia coli'\n/ FP /^ Taxlist: \(6\)\n/ FP /^ 'Escherichia coli'\n/ FP /^ 'Bacteria'\n/ FP /^ 'Proteobacteria'\n/ FP /^ 'gamma subdivision'\n/ FP /^ 'Enterobacteriaceae'\n/ FP /^ 'Escherichia'\n/ FP /^ Type: 'N'\n/ FP /^ Usa: 'debug::test.out'\n/ FP /^ Input format: 'embl'\n/ FP /^ Ufo: ''\n/ FP /^ Entryname: 'EMBL'\n/ FP /^ File name: 'test\.out'\n/ FP /^ Extension: 'fasta'\n/ FP /^ Single: 'No'\n/ FP /^ Features: 'No'\n/ FP /^ Count: 'No'\n/ FP /^ 51 gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 100\n/ // ID seqret-out-debug AP seqret CL -auto ../../data/dna.embl test.out -osf debug FI test.out FZ = 856 FP /^ Name: 'EMBL'\n/ FP /^ Accession: 'E10002'\n/ FP /^ SeqVersion: 'E10002.34'\n/ FP /^ GenInfo Id: ''\n/ FP /^ Description: 'EMBL FORMAT DNA SEQUENCE'\n/ FP /^ Keywordlist: \(2\)\n/ FP /^ 'DNA binding protein'\n/ FP /^ 'repressor'\n/ FP /^ Taxonomy: 'Escherichia coli'\n/ FP /^ Taxlist: \(6\)\n/ FP /^ 'Escherichia coli'\n/ FP /^ 'Bacteria'\n/ FP /^ 'Proteobacteria'\n/ FP /^ 'gamma subdivision'\n/ FP /^ 'Enterobacteriaceae'\n/ FP /^ 'Escherichia'\n/ FP /^ Type: 'N'\n/ FP /^ Usa: 'test.out'\n/ FP /^ Input format: 'embl'\n/ FP /^ Ufo: ''\n/ FP /^ Entryname: 'EMBL'\n/ FP /^ File name: 'test\.out'\n/ FP /^ Extension: 'debug'\n/ FP /^ Single: 'No'\n/ FP /^ Features: 'No'\n/ FP /^ Count: 'No'\n/ FP /^ 51 gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 100\n/ // ID seqret-outusa-embl AP seqret CL -auto ../../data/dna.embl embl::test.out FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^AC E10002;\n/ FP /^SV E10002.34\n/ FP /^DE EMBL FORMAT DNA SEQUENCE\n/ FP /^KW DNA binding protein; repressor.\n/ FP /^OS Escherichia coli\n/ FP /^OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^OC Escherichia.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 60\n/ // ID seqret-out-embl AP seqret CL -auto ../../data/dna.embl test.out -osf embl FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^AC E10002;\n/ FP /^SV E10002.34\n/ FP /^DE EMBL FORMAT DNA SEQUENCE\n/ FP /^KW DNA binding protein; repressor.\n/ FP /^OS Escherichia coli\n/ FP /^OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^OC Escherichia.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 60\n/ // ID seqret-outusa-experiment AP seqret CL -auto ../../data/dna.embl experiment::test.out FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP.\n/ FP /^\s+ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\s+100\n/ // ID seqret-out-experiment AP seqret CL -auto ../../data/dna.embl test.out -osf experiment FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP.\n/ FP /^\s+ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\s+100\n/ // ID seqret-outusa-fasta AP seqret CL -auto ../../data/dna.embl fasta::test.out FI test.out FZ = 143 FP /^>EMBL E10002.34 EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-out-fasta AP seqret CL -auto ../../data/dna.embl test.out -osf fasta FI test.out FZ = 143 FP /^>EMBL E10002.34 EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-outusa-fitch AP seqret CL -auto ../../data/dna.embl fitch::test.out FI test.out FZ = 152 FP /^EMBL, 100 bases\n/ FP /^ acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt\n/ // ID seqret-out-fitch AP seqret CL -auto ../../data/dna.embl test.out -osf fitch FI test.out FZ = 152 FP /^EMBL, 100 bases\n/ FP /^ acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt\n/ // ID seqret-outusa-gcg AP seqret CL -auto ../../data/dna.embl gcg::test.out FI test.out FZ = 211 FP /^\!\!NA_SEQUENCE 1\.0\n/ FP /^EMBL Length: 100 Type: N Check: 6856 \.\.\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac\n/ // ID seqret-out-gcg AP seqret CL -auto ../../data/dna.embl test.out -osf gcg FI test.out FZ = 211 FP /^\!\!NA_SEQUENCE 1\.0\n/ FP /^EMBL Length: 100 Type: N Check: 6856 \.\.\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac\n/ // ID seqret-outusa-genbank AP seqret CL -auto ../../data/dna.embl genbank::test.out FI test.out FZ = 489 FP /^LOCUS EMBL\n/ FP /^DEFINITION EMBL FORMAT DNA SEQUENCE\n/ FP /^ACCESSION E10002\n/ FP /^VERSION E10002.34\n/ FP /^KEYWORDS DNA binding protein; repressor.\n/ FP /^SOURCE Escherichia coli.\n/ FP /^ ORGANISM Escherichia coli\n/ FP /^ Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^ Escherichia.\n/ FP /^BASE COUNT 25 a 25 c 25 g 25 t\n/ FP /^ORIGIN\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\n/ // ID seqret-out-genbank AP seqret CL -auto ../../data/dna.embl test.out -osf genbank FI test.out FZ = 489 FP /^LOCUS EMBL\n/ FP /^DEFINITION EMBL FORMAT DNA SEQUENCE\n/ FP /^ACCESSION E10002\n/ FP /^VERSION E10002.34\n/ FP /^KEYWORDS DNA binding protein; repressor.\n/ FP /^SOURCE Escherichia coli.\n/ FP /^ ORGANISM Escherichia coli\n/ FP /^ Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^ Escherichia.\n/ FP /^BASE COUNT 25 a 25 c 25 g 25 t\n/ FP /^ORIGIN\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\n/ // ID seqret-outusa-gff AP seqret CL -auto ../../data/dna.embl gff::test.out FI test.out FZ = 191 FP /^##gff-version 2\n/ FP /^##source-version EMBOSS [0-9.]+\n/ FP /^##date [0-9\-]+\n/ FP /^##DNA EMBL\n/ FP /^##acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ FP /^##end-DNA\n/ // ID seqret-out-gff AP seqret CL -auto ../../data/dna.embl test.out -osf gff FI test.out FZ = 191 FP /^##gff-version 2\n/ FP /^##source-version EMBOSS [0-9.]+\n/ FP /^##date [0-9\-]+\n/ FP /^##DNA EMBL\n/ FP /^##acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ FP /^##end-DNA\n/ // ID seqret-outusa-ig AP seqret CL -auto ../../data/dna.embl ig::test.out FI test.out FZ = 145 FP /;EMBL FORMAT DNA SEQUENCE, 100 bases\n/ FP /EMBL\n/ FP /gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt1\n/ // ID seqret-out-ig AP seqret CL -auto ../../data/dna.embl test.out -osf ig FI test.out FZ = 145 FP /;EMBL FORMAT DNA SEQUENCE, 100 bases\n/ FP /EMBL\n/ FP /gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt1\n/ // ID seqret-outusa-ncbi AP seqret CL -auto ../../data/dna.embl ncbi::test.out FI test.out FZ = 153 FP /^>gnl\|unk\|EMBL \(E10002.34\) EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-out-ncbi AP seqret CL -auto ../../data/dna.embl test.out -osf ncbi FI test.out FZ = 153 FP /^>gnl\|unk\|EMBL \(E10002.34\) EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-outusa-staden AP seqret CL -auto ../../data/dna.embl staden::test.out FI test.out FZ = 113 FP // FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-out-staden AP seqret CL -auto ../../data/dna.embl test.out -osf staden FI test.out FZ = 113 FP // FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-outusa-strider AP seqret CL -auto ../../data/dna.embl strider::test.out FI test.out FZ = 166 FP /^; ### from DNA Strider ;-\)\n/ FP /^; DNA sequence EMBL, 100 bases\n/ FP /^;\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtac\n/ // ID seqret-out-strider AP seqret CL -auto ../../data/dna.embl test.out -osf strider FI test.out FZ = 166 FP /^; ### from DNA Strider ;-\)\n/ FP /^; DNA sequence EMBL, 100 bases\n/ FP /^;\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtac\n/ // ID seqret-outusa-swiss AP seqret CL -auto ../../data/dna.embl swiss::test.out FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^AC E10002;\n/ FP /^SV E10002.34\n/ FP /^DE EMBL FORMAT DNA SEQUENCE\n/ FP /^KW DNA binding protein; repressor.\n/ FP /^OS Escherichia coli\n/ FP /^OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^OC Escherichia.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 60\n/ // ID seqret-out-swiss AP seqret CL -auto ../../data/dna.embl test.out -osf swiss FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^AC E10002;\n/ FP /^SV E10002.34\n/ FP /^DE EMBL FORMAT DNA SEQUENCE\n/ FP /^KW DNA binding protein; repressor.\n/ FP /^OS Escherichia coli\n/ FP /^OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^OC Escherichia.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 60\n/ // ID seqret-outusa-text AP seqret CL -auto ../../data/dna.embl text::test.out FI test.out FZ = 102 FP /^gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-out-text AP seqret CL -auto ../../data/dna.embl test.out -osf text FI test.out FZ = 102 FP /^gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seqret-outmultiusa-acedb AP seqret CL -auto ../../data/dna.m-embl acedb::test.out FI test.out FZ = 420 FP 3 /^DNA : "FASTAM[1-3]"/ // ID seqret-outmulti-acedb AP seqret CL -auto ../../data/dna.m-embl test.out -osf acedb FI test.out FZ = 420 FP 3 /^DNA : "FASTAM[1-3]"/ // ID seqret-outmultiusa-asn1 AP seqret CL -auto ../../data/dna.m-embl asn1::test.out FI test.out FZ = 957 FP 3 /^ id \{ local id 1 \},/ FP 3 /^ descr { title "FASTA FORMAT DNA SEQUENCE F3000[1-3]" },\n/ FP /^ descr { title "FASTA FORMAT DNA SEQUENCE F30003" },\n/ // ID seqret-outmulti-asn1 AP seqret CL -auto ../../data/dna.m-embl test.out -osf asn1 FI test.out FZ = 957 FP 3 /^ id \{ local id 1 \},/ FP 3 /^ descr { title "FASTA FORMAT DNA SEQUENCE F3000[1-3]" },\n/ FP /^ descr { title "FASTA FORMAT DNA SEQUENCE F30003" },\n/ // ID seqret-outmultiusa-clustal AP seqret CL -auto ../../data/dna.m-embl clustal::test.out FI test.out FZ = 732 FP /^CLUSTAL W\(1\.4\) multiple sequence alignment\n/ FP /^FASTAM2 ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTAC\n/ // ID seqret-outmulti-clustal AP seqret CL -auto ../../data/dna.m-embl test.out -osf clustal FI test.out FZ = 732 FP /^CLUSTAL W\(1\.4\) multiple sequence alignment\n/ FP /^FASTAM2 ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTAC\n/ // ID seqret-outmultiusa-clustalprot AP seqret CL -auto ../../data/prot.m-swiss clustal::test.out FI test.out FZ = 583 FP /^CLUSTAL W\(1\.4\) multiple sequence alignment\n/ FP /^SWISSM2 AACCDDEEFFGGHHIIKKLLMMNNPPQQRRSSTTVVWWYYAACCDDEEFF\n/ FP 4 /^\n/ FP 2 /^ \n/ // ID seqret-outmulti-clustalprot AP seqret CL -auto ../../data/prot.m-swiss test.out -osf clustal FI test.out FZ = 583 FP /^CLUSTAL W\(1\.4\) multiple sequence alignment\n/ FP /^SWISSM2 AACCDDEEFFGGHHIIKKLLMMNNPPQQRRSSTTVVWWYYAACCDDEEFF\n/ FP 4 /^\n/ FP 2 /^ \n/ // ID seqret-outmultiusa-codata AP seqret CL -auto ../../data/dna.m-embl codata::test.out FI test.out FZ = 1410 FP 3 /^ENTRY FASTAM[1-3] \n/ FP 3 /^\/\/\/\n/ // ID seqret-outmulti-codata AP seqret CL -auto ../../data/dna.m-embl test.out -osf codata FI test.out FZ = 1410 FP 3 /^ENTRY FASTAM[1-3] \n/ FP 3 /^\/\/\/\n/ // ID seqret-outmultiusa-debug AP seqret CL -auto ../../data/dna.m-embl debug::test.out FI test.out FZ = 2150 FP 3 /^ Name: 'FASTAM[1-3]'\n/ FP 3 /^ Accession: 'F3000[1-3]'\n/ FP /^ Entryname: 'FASTAM3'\n/ FP 3 /^ Usa: 'debug::test.out'\n/ FP 3 /^ Input format: 'embl'\n/ FP 3 /^ Ufo: ''\n/ FP 3 /^ Entryname: 'FASTAM[1-3]'\n/ FP 3 /^ File name: 'test\.out'\n/ FP 3 /^ Extension: 'fasta'\n/ // ID seqret-outmulti-debug AP seqret CL -auto ../../data/dna.m-embl test.out -osf debug FI test.out FZ = 2129 FP 3 /^ Name: 'FASTAM[1-3]'\n/ FP 3 /^ Accession: 'F3000[1-3]'\n/ FP /^ Entryname: 'FASTAM3'\n/ FP 3 /^ Usa: 'test.out'\n/ FP 3 /^ Input format: 'embl'\n/ FP 3 /^ Ufo: ''\n/ FP 3 /^ Entryname: 'FASTAM[1-3]'\n/ FP 3 /^ File name: 'test\.out'\n/ FP 3 /^ Extension: 'debug'\n/ // ID seqret-outmultiusa-embl AP seqret CL -auto ../../data/dna.m-embl embl::test.out FI test.out FZ = 945 FP 3 /^ID FASTAM[1-3] standard; DNA; UNC; 120 BP.\n/ FP 3 /^AC F3000[1-3];\n/ FP /^AC F30003;\n/ FP /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;\n/ // ID seqret-outmulti-embl AP seqret CL -auto ../../data/dna.m-embl test.out -osf embl FI test.out FZ = 945 FP 3 /^ID FASTAM[1-3] standard; DNA; UNC; 120 BP.\n/ FP 3 /^AC F3000[1-3];\n/ FP /^AC F30003;\n/ FP /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;\n/ // ID seqret-outmultiusa-fasta AP seqret CL -auto ../../data/dna.m-embl fasta::test.out FI test.out FZ = 513 FP 3 /^>FASTAM[1-3] F3000[1-3] FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>FASTAM3 F30003 FASTA FORMAT DNA SEQUENCE F30003\n/ // ID seqret-outmulti-fasta AP seqret CL -auto ../../data/dna.m-embl test.out -osf fasta FI test.out FZ = 513 FP 3 /^>FASTAM[1-3] F3000[1-3] FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>FASTAM3 F30003 FASTA FORMAT DNA SEQUENCE F30003\n/ // ID seqret-outmultiusa-fitch AP seqret CL -auto ../../data/dna.m-embl fitch::test.out FI test.out FZ = 543 FP 3 /^FASTAM[1-3], 120 bases\n/ FP /^FASTAM1, 120 bases\n/ FP /^ ACG TAC GTA CGT ACG TAC GT- --- ACG TAC GTA CGT ACG TAC GTA CGT ACG TAC GTA CGT\n/ // ID seqret-outmulti-fitch AP seqret CL -auto ../../data/dna.m-embl test.out -osf fitch FI test.out FZ = 543 FP 3 /^FASTAM[1-3], 120 bases\n/ FP /^FASTAM1, 120 bases\n/ FP /^ ACG TAC GTA CGT ACG TAC GT- --- ACG TAC GTA CGT ACG TAC GTA CGT ACG TAC GTA CGT\n/ // ID seqret-outmultiusa-gcg AP seqret CL -auto ../../data/dna.m-embl gcg::test.out FI test.out FZ = 750 FP 3 /^!!NA_SEQUENCE 1\.0\n/ FP /^FASTAM1 Length: 120 Type: N Check: 8587 \.\.\n/ FP /^FASTAM2 Length: 120 Type: N Check: 6178 \.\.\n/ FP /^FASTAM3 Length: 120 Type: N Check: 8431 \.\.\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ // ID seqret-outmulti-gcg AP seqret CL -auto ../../data/dna.m-embl test.out -osf gcg FI test.out FZ = 750 FP 3 /^!!NA_SEQUENCE 1\.0\n/ FP /^FASTAM1 Length: 120 Type: N Check: 8587 \.\.\n/ FP /^FASTAM2 Length: 120 Type: N Check: 6178 \.\.\n/ FP /^FASTAM3 Length: 120 Type: N Check: 8431 \.\.\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ // ID seqret-outmultiusa-genbank AP seqret CL -auto ../../data/dna.m-embl genbank::test.out FI test.out FZ = 899 FP 3 /^LOCUS FASTAM[1-3]\n/ FP /^LOCUS FASTAM3\n/ FP 3 /^ACCESSION F3000[1-3]\n/ FP /^ACCESSION F30003\n/ FP /^BASE COUNT 29 a 29 c 29 g 29 t 4 others\n/ FP 3 /^\/\/\n/ // ID seqret-outmulti-genbank AP seqret CL -auto ../../data/dna.m-embl test.out -osf genbank FI test.out FZ = 899 FP 3 /^LOCUS FASTAM[1-3]\n/ FP /^LOCUS FASTAM3\n/ FP 3 /^ACCESSION F3000[1-3]\n/ FP /^ACCESSION F30003\n/ FP /^BASE COUNT 29 a 29 c 29 g 29 t 4 others\n/ FP 3 /^\/\/\n/ // ID seqret-outmultiusa-gff AP seqret CL -auto ../../data/dna.m-embl gff::test.out FI test.out FZ = 642 FP 3 /^##DNA FASTAM[1-3]\n/ FP /^##DNA FASTAM2\n/ FP 3 /^##end-DNA\n/ // ID seqret-outmulti-gff AP seqret CL -auto ../../data/dna.m-embl test.out -osf gff FI test.out FZ = 642 FP 3 /^##DNA FASTAM[1-3]\n/ FP /^##DNA FASTAM2\n/ FP 3 /^##end-DNA\n/ // ID seqret-outmultiusa-gffprot AP seqret CL -auto ../../data/prot.m-swiss gff::test.out FI test.out FZ = 543 FP 3 /^##gff-version 2\n/ FP 3 /^##Protein SWISSM[1-3]\n/ FP /^##Protein SWISSM2\n/ FP 3 /^##end-Protein\n/ FP /^##MMNNPPQQRRSSTTVVWWYY\n/ // ID seqret-outmulti-gffprot AP seqret CL -auto ../../data/prot.m-swiss test.out -osf gff FI test.out FZ = 543 FP 3 /^##gff-version 2\n/ FP 3 /^##Protein SWISSM[1-3]\n/ FP /^##Protein SWISSM2\n/ FP 3 /^##end-Protein\n/ FP /^##MMNNPPQQRRSSTTVVWWYY\n/ // ID seqret-outmultiusa-hennig86 AP seqret CL -auto ../../data/dna.m-embl hennig86::test.out FI test.out FZ = 432 FP /^xread\n/ FP /^' Written by EMBOSS [0-9][0-9]\/[01][0-9]\/[0-9][0-9] '\n/ FP /^120 3\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^03210321032103210321\?\?\?\?032103210321032103210321032103210321032103210321032103210321032103210321032103210321123003210321\n/ FP /^;\n/ // ID seqret-outmulti-hennig86 AP seqret CL -auto ../../data/dna.m-embl test.out -osf hennig86 FI test.out FZ = 432 FP /^xread\n/ FP /^' Written by EMBOSS [0-9][0-9]\/[01][0-9]\/[0-9][0-9] '\n/ FP /^120 3\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^03210321032103210321\?\?\?\?032103210321032103210321032103210321032103210321032103210321032103210321032103210321123003210321\n/ FP /^;\n/ // ID seqret-outmultiusa-jackknifer AP seqret CL -auto ../../data/dna.m-embl jackknifer::test.out FI test.out FZ = 590 FP /^' Written by EMBOSS [0-9\/]+ \n/ FP 3 /^\(FASTAM3\) [ACGT\-]+\n/ // ID seqret-outmulti-jackknifer AP seqret CL -auto ../../data/dna.m-embl test.out -osf jackknifer FI test.out FZ = 590 FP /^' Written by EMBOSS [0-9\/]+ \n/ FP 3 /^\(FASTAM3\) [ACGT\-]+\n/ // ID seqret-outmultiusa-mega AP seqret CL -auto ../../data/dna.m-embl mega::test.out FI test.out FZ = 610 FP /^#mega\n/ FP /^TITLE: Written by EMBOSS [0-9\/]+\n/ FP 9 /^#FASTAM[1-3] [ACGT\-]+\n/ FP 3 /^\n/ // ID seqret-outmulti-mega AP seqret CL -auto ../../data/dna.m-embl test.out -osf mega FI test.out FZ = 610 FP /^#mega\n/ FP /^TITLE: Written by EMBOSS [0-9\/]+\n/ FP 9 /^#FASTAM[1-3] [ACGT\-]+\n/ FP 3 /^\n/ // ID seqret-outmultiusa-meganon AP seqret CL -auto ../../data/dna.m-embl meganon::test.out FI test.out FZ = 470 FP /^#mega\n/ FP /^TITLE: Written by EMBOSS [0-9\/]+\n/ FP /^#FASTAM2 \n/ FP 3 /^#FASTAM[1-3] \n/ // ID seqret-outmulti-meganon AP seqret CL -auto ../../data/dna.m-embl test.out -osf meganon FI test.out FZ = 470 FP /^#mega\n/ FP /^TITLE: Written by EMBOSS [0-9\/]+\n/ FP /^#FASTAM2 \n/ FP 3 /^#FASTAM[1-3] \n/ // ID seqret-outmultiusa-msf AP seqret CL -auto ../../data/dna.m-embl msf::test.out FI test.out FZ = 880 FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 120 Type: N [0-9\/]+ CompCheck: 3196 \.\.\n/ FP /^ Name: FASTAM1 Len: 120 Check: 8587 Weight: 1\.00\n/ FP /^ Name: FASTAM2 Len: 120 Check: 6178 Weight: 1\.00\n/ FP /^ Name: FASTAM3 Len: 120 Check: 8431 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 3 /^FASTAM3 [ACGT\-]+\n/ // ID seqret-outmulti-msf AP seqret CL -auto ../../data/dna.m-embl test.out -osf msf FI test.out FZ = 880 FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 120 Type: N [0-9\/]+ CompCheck: 3196 \.\.\n/ FP /^ Name: FASTAM1 Len: 120 Check: 8587 Weight: 1\.00\n/ FP /^ Name: FASTAM2 Len: 120 Check: 6178 Weight: 1\.00\n/ FP /^ Name: FASTAM3 Len: 120 Check: 8431 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 3 /^FASTAM3 [ACGT\-]+\n/ // ID seqret-outmulti-msf-noalign AP seqret CL -auto tembl:paami\* test.out -osf msf FI test.out FZ = 13831 FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 2167 Type: N [0-9/]+ CompCheck: 9293 \.\.\n/ FP 4 /^ Name: PAAMI/ FP /^ 1 50\n/ FP 21 /^PAAMIE +[ACGTacgt\-]+\n/ FP 1 /^PAAMIE +[ACGTacgt\-]+[~]+\n/ FP 22 /^PAAMIE +[~]+\n/ // ID seqret-outmultiusa-msfprot AP seqret CL -auto ../../data/prot.m-swiss msf::test.out FI test.out FZ = 752 FP /^!!AA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 100 Type: P [0-9\/]+ CompCheck: 4147 \.\.\n/ FP /^ Name: SWISSM1 Len: 100 Check: 1414 Weight: 1\.00\n/ FP /^ Name: SWISSM2 Len: 100 Check: 1993 Weight: 1\.00\n/ FP /^ Name: SWISSM3 Len: 100 Check: 740 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 2 /^SWISSM2 [A-Z~]+\n/ // ID seqret-outmulti-msfprot AP seqret CL -auto ../../data/prot.m-swiss test.out -osf msf FI test.out FZ = 752 FP /^!!AA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 100 Type: P [0-9\/]+ CompCheck: 4147 \.\.\n/ FP /^ Name: SWISSM1 Len: 100 Check: 1414 Weight: 1\.00\n/ FP /^ Name: SWISSM2 Len: 100 Check: 1993 Weight: 1\.00\n/ FP /^ Name: SWISSM3 Len: 100 Check: 740 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 2 /^SWISSM2 [A-Z~]+\n/ // ID seqret-outmultiusa-nexus AP seqret CL -auto ../../data/dna.m-embl nexus::test.out FI test.out FZ = 756 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format interleave datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ FP 3 /^FASTAM2 [ACGT\-]+\n/ // ID seqret-outmulti-nexus AP seqret CL -auto ../../data/dna.m-embl test.out -osf nexus FI test.out FZ = 756 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format interleave datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ FP 3 /^FASTAM2 [ACGT\-]+\n/ // ID seqret-outmultiusa-nexusnon AP seqret CL -auto ../../data/dna.m-embl nexusnon::test.out FI test.out FZ = 572 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP 3 /^FASTAM[1-3]\n/ FP 3 /^[ACGT\-]+\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ // ID seqret-outmulti-nexusnon AP seqret CL -auto ../../data/dna.m-embl test.out -osf nexusnon FI test.out FZ = 572 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP 3 /^FASTAM[1-3]\n/ FP 3 /^[ACGT\-]+\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ // ID seqret-outmultiusa-phylip AP seqret CL -auto ../../data/dna.m-embl phylip::test.out FI test.out FZ = 495 FP /^ 3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ // ID seqret-outmulti-phylip AP seqret CL -auto ../../data/dna.m-embl test.out -osf phylip FI test.out FZ = 495 FP /^ 3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ // ID seqret-outmultiusa-phylipnon AP seqret CL -auto ../../data/dna.m-embl phylipnon::test.out FI test.out FZ = 492 FP /^3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ FP / GTACGTACGT\nFASTAM2/ // ID seqret-outmulti-phylipnon AP seqret CL -auto ../../data/dna.m-embl test.out -osf phylipnon FI test.out FZ = 492 FP /^3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ FP / GTACGTACGT\nFASTAM2/ // ID seqret-outmultiusa-swiss AP seqret CL -auto ../../data/prot.m-swiss swiss::test.out FI test.out FZ = 793 FP 3 /^ID SWISSM[1-3] STANDARD; PRT; +[0-9]+ AA\.\n/ FP /^ID SWISSM2 STANDARD; PRT; 80 AA\.\n/ FP /^SQ SEQUENCE 60 AA; 7151 MW; FF73258FFC19CF5B CRC64;/ FP 3 /^\/\/\n/ // ID seqret-outmulti-swiss AP seqret CL -auto ../../data/prot.m-swiss test.out -osf swiss FI test.out FZ = 793 FP 3 /^ID SWISSM[1-3] STANDARD; PRT; +[0-9]+ AA\.\n/ FP /^ID SWISSM2 STANDARD; PRT; 80 AA\.\n/ FP /^SQ SEQUENCE 60 AA; 7151 MW; FF73258FFC19CF5B CRC64;/ FP 3 /^\/\/\n/ // ID seqret-outmultiusa-ncbi AP seqret CL -auto ../../data/dna.m-embl ncbi::test.out FI test.out FZ = 543 FP 3 /^>gnl\|unk\|FASTAM[1-3] \(F3000[1-3]\) FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>gnl\|unk\|FASTAM2 \(F30002\) FASTA FORMAT DNA SEQUENCE F30002\n/ // ID seqret-outmulti-ncbi AP seqret CL -auto ../../data/dna.m-embl test.out -osf ncbi FI test.out FZ = 543 FP 3 /^>gnl\|unk\|FASTAM[1-3] \(F3000[1-3]\) FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>gnl\|unk\|FASTAM2 \(F30002\) FASTA FORMAT DNA SEQUENCE F30002\n/ // ID seqret-outmultiusa-nbrf AP seqret CL -auto ../../data/dna.m-embl nbrf::test.out FI test.out FZ = 579 FP 3 /^>D1;FASTAM[1-3]\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTA FORMAT DNA SEQUENCE F30001, 120 bases\n/ FP /^ ACGTACGTTG CAACGTACGT\*\n/ // ID seqret-outmulti-nbrf AP seqret CL -auto ../../data/dna.m-embl test.out -osf nbrf FI test.out FZ = 579 FP 3 /^>D1;FASTAM[1-3]\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTA FORMAT DNA SEQUENCE F30001, 120 bases\n/ FP /^ ACGTACGTTG CAACGTACGT\*\n/ // ID seqret-outmultiusa-ig AP seqret CL -auto ../../data/dna.m-embl ig::test.out FI test.out FZ = 531 FP /^;FASTA FORMAT DNA SEQUENCE F30002, 120 bases\n/ FP 3 /^;FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTAM2\n/ FP 3 /^FASTAM[1-3]\n/ FP /^ACGTACGTACGTACGTACGT1\n/ // ID seqret-outmulti-ig AP seqret CL -auto ../../data/dna.m-embl test.out -osf ig FI test.out FZ = 531 FP /^;FASTA FORMAT DNA SEQUENCE F30002, 120 bases\n/ FP 3 /^;FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTAM2\n/ FP 3 /^FASTAM[1-3]\n/ FP /^ACGTACGTACGTACGTACGT1\n/ // ID seqret-outmultiusa-strider AP seqret CL -auto ../../data/dna.m-embl strider::test.out FI test.out FZ = 570 FP /^; ### from DNA Strider ;-\)\n/ FP 3 /^; DNA sequence FASTAM[1-3], 120 bases\n/ FP /^; DNA sequence FASTAM2, 120 bases\n/ FP /^;\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seqret-outmulti-strider AP seqret CL -auto ../../data/dna.m-embl test.out -osf strider FI test.out FZ = 570 FP /^; ### from DNA Strider ;-\)\n/ FP 3 /^; DNA sequence FASTAM[1-3], 120 bases\n/ FP /^; DNA sequence FASTAM2, 120 bases\n/ FP /^;\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seqret-outmultiusa-treecon AP seqret CL -auto ../../data/dna.m-embl treecon::test.out FI test.out FZ = 391 FP /^120\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCAACGTACGT\n/ // ID seqret-outmulti-treecon AP seqret CL -auto ../../data/dna.m-embl test.out -osf treecon FI test.out FZ = 391 FP /^120\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCAACGTACGT\n/ // ID seqret-offset AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat%1753 FI test.out FZ = 4488 FP /^ID RNOPS / FP /^ID RNU68037 / FP 2 /^ID/ FI stderr FZ = 0 // ID seqret-offset-zero AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat%0 FI test.out FZ = 5457 FP /^ID MMAM / FP /^ID RNOPS / FP /^ID RNU68037 / FP 3 /^ID/ FI stderr FZ = 0 // ##################################################### # Test the query part of USAs ##################################################### ID seqret-query-direct-fail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:bad:MMAM FI stderr FZ = 207 FP /Error: Unknown query field 'bad' in USA '../../embl/rod.dat:bad:MMAM'/ FP /Error: Unable to read sequence 'embl::../../embl/rod.dat:bad:MMAM'/ FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / // ID seqret-query-direct-name AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:MMAM FI test.out FZ = 969 FP /^ID MMAM / FP 1 /^ID/ // ID seqret-query-direct-name2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:RNOPS FI test.out FZ = 2396 FP /^ID RNOPS / FP 1 /^ID/ // ID seqret-query-direct-namefail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:FAIL FI stderr FZ = 133 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:FAIL'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-id AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:id:MMAM FI test.out FZ = 969 FP /^ID MMAM / FP 1 /^ID/ // ID seqret-query-direct-id2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ID:RNOPS FI test.out FZ = 2396 FP /^ID RNOPS / FP 1 /^ID/ // ID seqret-query-direct-idfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ID:FAIL FI stderr FZ = 136 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:ID:FAIL'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-acc AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:L48662 FI test.out FZ = 969 FP /^ID MMAM / FP 1 /^ID/ // ID seqret-query-direct-acc2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:Z46957 FI test.out FZ = 2396 FP /^ID RNOPS / FP 1 /^ID/ // ID seqret-query-direct-accfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:Z99999 FI stderr FZ = 139 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:ACC:Z99999'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-accfail2 ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:99999Z FI stderr FZ = 139 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:ACC:99999Z'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-sv AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:SV:L48662* FI test.out FZ = 969 FP /^ID MMAM / FP 1 /^ID/ // ID seqret-query-direct-sv2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:SV:Z46957.1 FI test.out FZ = 2396 FP /^ID RNOPS / FP 1 /^ID/ // ID seqret-query-direct-svfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:SV:Z99999.1 FI stderr FZ = 140 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:SV:Z99999.1'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-des AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:*receptor* FI test.out FZ = 2092 FP /^ID RNU68037 / FP 1 /^ID/ // ID seqret-query-direct-des2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:*norvegicus* FI test.out FZ = 4488 FP /^ID RNOPS / FP 2 /^ID/ // ID seqret-query-direct-desfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:lynam FI stderr FZ = 138 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:DES:lynam'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-deswordstart AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:Mus FI test.out FZ = 969 FP /^ID MMAM / FP 1 /^ID/ // ID seqret-query-direct-deswordmid AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:mrna FI test.out FZ = 5457 FP /^ID RNOPS / FP 3 /^ID/ // ID seqret-query-direct-deswordend AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:receptor FI test.out FZ = 2092 FP /^ID RNU68037 / FP 1 /^ID/ // ID seqret-query-direct-key AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:KEY:rhodopsin FI test.out FZ = 2396 FP /^ID RNOPS / FP 1 /^ID/ // ID seqret-query-direct-keyfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:KEY:CHAIN FI stderr FZ = 138 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:KEY:CHAIN'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-org AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:Mus\* FI test.out FZ = 969 FP /^ID MMAM / FP 1 /^ID/ // ID seqret-query-direct-org2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:Rattus\* FI test.out FZ = 4488 FP /^ID RNOPS / FP /^ID RNU68037 / FP 2 /^ID/ // ID seqret-query-direct-org3 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:Rodentia FI test.out FZ = 5457 FP /^ID MMAM / FP /^ID RNOPS / FP /^ID RNU68037 / FP 3 /^ID/ // ID seqret-query-direct-orgfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:HOMO FI stderr FZ = 137 FP /^Error: Unable to read sequence 'embl::../../embl/rod.dat:ORG:HOMO'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-srs-badfield ER 1 CC No need for a local SRS installation - fails at USA processing CC Reports bad filename because 'bad' is an unknown field AP seqret CL -auto -out test.out -osf embl qasrs-bad:AB000095 FI stderr FZ = 205 FP /^Error: USA 'qasrs-bad:AB000095' query field 'bad' not defined for database 'qasrs'/ FP /^Error: Unable to read sequence 'qasrs-bad:AB000095'/ FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / // ID seqret-query-srs-badfield2 ER 1 CC No need for a local SRS installation - fails at USA processing CC Reports bad filename because 'key' is not defined in 'fields' for qasrs AP seqret CL -auto -out test.out -osf embl qasrs-key:AB000095 FI stderr FZ = 205 FP /^Error: USA 'qasrs-key:AB000095' query field 'key' not defined for database 'qasrs'/ FP /^Error: Unable to read sequence 'qasrs-key:AB000095'/ FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / // ID seqret-query-srs-id CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs-ID:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-acc CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs-ACC:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-sv CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs-SV:AB000095.1 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-name CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-fail CC Requires a local SRS installation RQ srs ER 1 AP seqret CL -auto -out test.out -osf embl qasrs-id:OLD FI stderr FZ = 116 FP /^Error: Unable to read sequence 'qasrs-id:OLD'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-srsfasta-id CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta-ID:AB000095 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-acc CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta-ACC:AB000095 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-sv CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta-SV:AB000095.1 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-name CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta:AB000095 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-fail CC Requires a local SRS installation RQ srs ER 1 AP seqret CL -auto -out test.out -osf embl qasrsfasta-id:OLD FI stderr FZ = 121 FP /^Error: Unable to read sequence 'qasrsfasta-id:OLD'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-srswww-id AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-ID:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srswww-acc AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-ACC:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srswww-sv AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-SV:AB000095.1 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srswww-name AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srswww-fail ER 1 AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-id:OLD FI stderr FZ = 119 FP /^Error: Unable to read sequence 'qasrswww-id:OLD'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // #################################################### # End of query USA tests #################################################### #################################################### # seqret examples for documentation #################################################### ID seqret-ex UC Extract an entry from a database and write it to a file: AP seqret IN tembl:hsfau IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.fasta FP /HSFAU/ // ID seqret-ex2 UC Display the contents of the sequence on the screen: AP seqret IN tembl:hsfau IN stdout FI stdout FP /HSFAU/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID seqret-ex3 UC Write the result in GCG format by using the qualifier '-osformat'. AP seqret CL -osf gcg IN tembl:hsfau IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.gcg FP /HSFAU/ // ID seqret-ex4 UC Write the result in GCG format by specifying the format UC in the output USA on the command line. AP seqret CL -outseq gcg::hsfau.gcg IN tembl:hsfau FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.gcg FP /HSFAU/ // ID seqret-ex5 UC Write the result in GCG format by specifying the format UC in the output USA at the prompt. AP seqret IN tembl:hsfau IN gcg::hsfau.gcg FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.gcg FP /HSFAU/ // ID seqret-ex6 UC Write the reverse-complement of a sequence: AP seqret CL -srev IN tembl:hsfau IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.fasta FP /HSFAU/ // ID seqret-ex7 UC Extract the bases between the positions starting at 5 and ending at 25: AP seqret CL -sbegin 5 -send 25 IN tembl:hsfau IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.fasta FP /HSFAU/ // ID seqret-ex8 UC Extract the bases between the positions starting at 5 UC and ending at 5 bases before the end of the sequence: AP seqret CL -sbegin 5 -send -5 IN tembl:hsfau IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.fasta FP /HSFAU/ // ID seqret-ex9 UC Read all entries in the database 'tembl' that start with 'hs' UC and write them to a file: AP seqret IN tembl:hs* IN hsall.seq FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsall.seq FP /HSFAU/ // ID seqret-ex10 UC Read all entries in the database 'tembl' that start with 'hs' UC and write them to a file. UC In this example the specification is all done in the command line UC and to stop Unix getting confused by the '*' character, UC it has to have a backslash ('\') before it: AP seqret CL tembl:hs\* hsall.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsall.seq FP /HSFAU/ // ID seqret-ex11 UC seqret does not read in features by default because this results in UC slightly faster performance. If however you wish to read in features UC with your sequence and write them out on output, using '-feature' will UC change the default behaviour to use any features present in the sequence. UC N.B. use embl format for the output file as the default format 'fasta' UC reports the features in gff (file ".gff") AP seqret CL -feature IN tembl:hsfau IN embl::hsfau.embl FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.embl FP /HSFAU/ // #################################################### # end of seqret examples for documentation #################################################### ID seqretall-ex AP seqret CL -auto tembl:eclac* test.out -osf fasta FI test.out FZ = 15618 FP 5 /^>ECLAC/ FP 5 /^>/ // ID seqretall-ex1 AP seqret CL -auto tembl:eclacz test.out -osf fasta FI test.out FP 1 /^>ECLAC/ // ############################################################################# # should make output filename optional as it is rarely used ID seqretsplit-ex AP seqretsplit CL tembl:hsfa* IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.fasta FZ = 562 FP /^>HSFAU / FI hsfau1.fasta FZ = 2088 FP /^>HSFAU1 / // ##################################################### # Testing NCBI formatted ID lines are correctly split ##################################################### ID seqret-ncbi-gb AP seqret CL ../../data/testids.ncbi:GENBANK test.out -auto FI test.out FP 1 /^>/ FP /^>GENBANK G12345 / FP /^GENBANK$/ FZ = 58 // ID seqret-ncbi-embl AP seqret CL ../../data/testids.ncbi:EMBL test.out -auto FI test.out FP 1 /^>/ FP /^>EMBL E12345 / FP /^EMBL$/ FZ = 49 // ID seqret-ncbi-ddbj AP seqret CL ../../data/testids.ncbi:DDBJ test.out -auto FI test.out FP 1 /^>/ FP /^>DDBJ D12345 / FP /^DDB-$/ FZ = 49 // ID seqret-ncbi-pir AP seqret CL ../../data/testids.ncbi:PIR test.out -auto FI test.out FP 1 /^>/ FP /^>PIR PIR/ FP /^PIR$/ FZ = 40 // ID seqret-ncbi-prf AP seqret CL ../../data/testids.ncbi:PRF test.out -auto FI test.out FP 1 /^>/ FP /^>PRF Protein / FP /^PRF$/ FZ = 58 // ID seqret-ncbi-swissprt AP seqret CL ../../data/testids.ncbi:SWISS_PRT test.out -auto FI test.out FP 1 /^>/ FP /^>SWISS_PRT P01234/ FP /^SWISSPR-T$/ FZ = 64 // ID seqret-ncbi-pdb AP seqret CL ../../data/testids.ncbi:2PDBA test.out -auto FI test.out FP 1 /^>/ FP /^>2PDBA PDB / FP /^-PDB-A$/ FZ = 35 // ID seqret-ncbi-pat AP seqret CL ../../data/testids.ncbi:12345 test.out -auto FI test.out FP 1 /^>/ FP /^>12345 Patent/ FP /^PAT-K$/ FZ = 39 // ID seqret-ncbi-bbs AP seqret CL ../../data/testids.ncbi:GENINFO test.out -auto FI test.out FP 1 /^>/ FP /^>geninfo Geninfo/ FP /^GENINF-$/ FZ = 37 // ID seqret-ncbi-gnl AP seqret CL ../../data/testids.ncbi:E1234 test.out -auto FI test.out FP 1 /^>/ FP /^>e1234 General/ FP /^GNLPID$/ FZ = 68 // ID seqret-ncbi-ref1 AP seqret CL ../../data/testids.ncbi:REF_12345 test.out -auto FI test.out FP 1 /^>/ FP /^>REF_12345 NP_007225[.]1 / FP /^REFSEQ$/ FZ = 54 // ID seqret-ncbi-ref2 AP seqret CL ../../data/testids.ncbi:NM_012488.1 test.out -auto FI test.out FP 1 /^>/ FP /^>NM_012488[.]1 NM_012488[.]1 / FP /^REFSEQ$/ FZ = 70 // ID seqret-ncbi-lcl AP seqret CL ../../data/testids.ncbi:LOCALID test.out -auto FI test.out FP 1 /^>/ FP /^>localid Local / FP /^L-CALID$/ FZ = 53 // ID seqret-ncbi-gi AP seqret CL ../../data/testids.ncbi:123456 test.out -auto FI test.out FP 1 /^>/ FP /^>123456 gi prefix/ FP /^GIPREFIX$/ FZ = 27 // ID seqret-ncbi-gigb AP seqret CL ../../data/testids.ncbi:GIGENBANK test.out -auto FI test.out FP 1 /^>/ FP /^>GIGENBANK G67890 / FP /^GIGENBANK$/ FZ = 52 // ID seqret-ncbi-gisp AP seqret CL ../../data/testids.ncbi:GISWISS_PRT test.out -auto FI test.out FP 1 /^>/ FP /^>GISWISS_PRT P01234 / FP /^GISWISSPR-T$/ FZ = 58 // ID seqret-ncbi-gnlblast AP seqret CL ../../data/testids.ncbi:BLAST test.out -auto FI test.out FP 1 /^>/ FP /^>blast formatdb / FP /^BLAST$/ FZ = 46 // ############################################### # seqret (sequence input) associated qualifiers ############################################### ID seq-end-fasta AQ seqretsingle CL tembl:eclaci -send 100 -out test.out -auto FI test.out FZ = 168 FP 1 /^>/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-begin-fasta AQ seqretsingle CL tembl:eclaci -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 117 FP 1 /^>/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-rev-fasta AQ seqretsingle CL tembl:eclaci -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 117 FP 1 /^>/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seq-end-msf AQ seqretsingle CL tembl:eclaci -send 100 -out test.out -osf msf -auto FI test.out FZ = 395 FP 1 /^ +Name: / FP / +Name: ECLACI .* Check: 8066/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-begin-msf AQ seqretsingle CL tembl:eclaci -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: ECLACI .* Check: 2937/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-rev-msf AQ seqretsingle CL tembl:eclaci -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: ECLACI .* Check: 9768/ FP /^ECLACI ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seqall-end-fasta AP seqret CL tembl:eclac\* -send 100 -out test.out -auto FI test.out FZ = 876 FP 5 /^>/ FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqall-begin-fasta AP seqret CL tembl:eclac\* -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqall-rev-fasta AP seqret CL tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seqall-end-msf AP seqret CL tembl:eclac\* -send 100 -out test.out -osf msf -auto FI test.out FZ = 1107 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 4203/ FP / +Name: ECLACI .* Check: 8066/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqall-begin-msf AP seqret CL tembl:eclac\* -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 1328/ FP / +Name: ECLACI .* Check: 2937/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqall-rev-msf AP seqret CL tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 2885/ FP / +Name: ECLACI .* Check: 9768/ FP /^ECLAC cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ECLACI ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seqset-end-fasta AQ seqretset CL tembl:eclac\* -send 100 -out test.out -auto FI test.out FZ = 876 FP 5 /^>/ FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqset-begin-fasta AQ seqretset CL tembl:eclac\* -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqset-rev-fasta AQ seqretset CL tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seqset-end-msf AQ seqretset CL tembl:eclac\* -send 100 -out test.out -osf msf -auto FI test.out FZ = 1107 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 4203/ FP / +Name: ECLACI .* Check: 8066/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqset-begin-msf AQ seqretset CL tembl:eclac\* -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 1328/ FP / +Name: ECLACI .* Check: 2937/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqset-rev-msf AQ seqretset CL tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 2885/ FP / +Name: ECLACI .* Check: 9768/ FP /^ECLAC cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ECLACI ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ###################################################### # end of seqret (sequence input) associated qualifiers ###################################################### ########################################################### # seqret (sequence and feature input) associated qualifiers ########################################################### ID featseq-end-fasta AQ seqretsingle CL -feat tembl:eclaci -send 100 -out test.out -auto FI test.out FZ = 168 FP 1 /^>/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 724 FP /^##Type DNA ECLACI\n/ FP /^ECLACI\tEMBL\tCDS\t31\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2"/ // ID featseq-begin-fasta AQ seqretsingle CL -feat tembl:eclaci -sbegin 51 -send 100 -out test.out -auto FI test.out FP 1 /^>/ FZ = 117 FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 721 FP /^##Type DNA ECLACI\n/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x3"/ // ID featseq-rev-fasta AQ seqretsingle CL -feat tembl:eclaci -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 117 FP 1 /^>/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 721 FP /^##Type DNA ECLACI\n/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[-]\t[.].*FeatFlags "0x3"/ // ID featseq-end-embl AQ seqretsingle CL -feat tembl:eclaci -send 100 -out test.out -osf embl -auto FI test.out FZ = 1393 FP 1 /^ID / FP 1 /^FH / FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/ FP /^FT CDS 31..>100\n/ // ID featseq-begin-embl AQ seqretsingle CL -feat tembl:eclaci -sbegin 51 -send 100 -out test.out -osf embl -auto FI test.out FZ = 1308 FP 1 /^ID / FP 1 /^FH / FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/ FP /^FT CDS <1..>50\n/ // ID featseq-rev-embl AQ seqretsingle CL -feat tembl:eclaci -sbegin 51 -send 100 -srev -out test.out -osf embl -auto FI test.out FZ = 1332 FP 1 /^ID / FP 1 /^FH / FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/ FP /^FT CDS complement[(]<1..>50[)]\n/ // ID featseq-end-msf AQ seqretsingle CL -feat tembl:eclaci -send 100 -out test.out -osf msf -auto FI test.out FZ = 395 FP 1 /^ +Name: / FP / +Name: ECLACI .* Check: 8066/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 724 FP /^##Type DNA ECLACI\n/ FP /^ECLACI\tEMBL\tCDS\t31\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2"/ // ID featseq-begin-msf AQ seqretsingle CL -feat tembl:eclaci -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: ECLACI .* Check: 2937/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 721 FP /^##Type DNA ECLACI\n/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x3"/ // ID featseq-rev-msf AQ seqretsingle CL -feat tembl:eclaci -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: ECLACI .* Check: 9768/ FP /^ECLACI ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 721 FP /^##Type DNA ECLACI\n/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[-]\t[.].*FeatFlags "0x3"/ // ID featseqall-end-fasta AP seqret CL -feat tembl:eclac\* -send 100 -out test.out -auto FI test.out FZ = 876 FP 5 /^>/ FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4450 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t79\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t31\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2"/ // ID featseqall-begin-fasta AP seqret CL -feat tembl:eclac\* -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t29\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x3"/ // ID featseqall-rev-fasta AP seqret CL -feat tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t1\t22\t0[.]000\t[-]\t[.].*FeatFlags "0x1" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[-]\t[.].*FeatFlags "0x3"/ // ID featseqall-end-embl AP seqret CL -feat tembl:eclac\* -send 100 -out test.out -osf embl -auto FI test.out FZ = 8202 FP 5 /^ID / FP 5 /^FH / FP /^ +caattcaggg tggtgaatgt gaaaccagta acgttatacg +100\n/ FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/ FP /^FT CDS 31..>100\n/ // ID featseqall-begin-embl AP seqret CL -feat tembl:eclac\* -sbegin 51 -send 100 -out test.out -osf embl -auto FI test.out FZ = 7381 FP 5 /^ID / FP 5 /^FH / FP /^ +ggaagagagt caattcaggg tggtgaatgt gaaaccagta acgttatacg +50/ FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/ FP /^FT CDS 29..>50\n/ FP /^FT CDS <1..>50\n/ // ID featseqall-rev-embl AP seqret CL -feat tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -osf embl -auto FI test.out FZ = 7525 FP 5 /^ID / FP 5 /^FH / FP /^ +cgtataacgt tactggtttc acattcacca ccctgaattg actctcttcc +50\n/ FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/ FP /^FT CDS complement[(]<1..22[)]\n/ FP /^FT CDS complement[(]<1..>50[)]\n/ // ID featseqall-end-msf AP seqret CL -feat tembl:eclac\* -send 100 -out test.out -osf msf -auto FI test.out FZ = 1107 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 4203/ FP / +Name: ECLACI .* Check: 8066/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4450 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t79\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t31\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2"/ // ID featseqall-begin-msf AP seqret CL -feat tembl:eclac\* -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 1328/ FP / +Name: ECLACI .* Check: 2937/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t29\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x3"/ // ID featseqall-rev-msf AP seqret CL -feat tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 2885/ FP / +Name: ECLACI .* Check: 9768/ FP /^ECLAC cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ECLACI ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t1\t22\t0[.]000\t[-]\t[.].*FeatFlags "0x1" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[-]\t[.].*FeatFlags "0x3"/ // ID featseqset-end-fasta AQ seqretset CL -feat tembl:eclac\* -send 100 -out test.out -auto FI test.out FZ = 876 FP 5 /^>/ FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4450 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t79\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t31\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2"/ // ID featseqset-begin-fasta AQ seqretset CL -feat tembl:eclac\* -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t29\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x3"/ // ID featseqset-rev-fasta AQ seqretset CL -feat tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 621 FP 5 /^>/ FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t1\t22\t0[.]000\t[-]\t[.].*FeatFlags "0x1" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[-]\t[.].*FeatFlags "0x3"/ // ID featseqset-end-embl AQ seqretset CL -feat tembl:eclac\* -send 100 -out test.out -osf embl -auto FI test.out FZ = 8202 FP 5 /^ID / FP 5 /^FH / FP /^ +caattcaggg tggtgaatgt gaaaccagta acgttatacg +100\n/ FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/ FP /^FT CDS 31..>100\n/ // ID featseqset-begin-embl AQ seqretset CL -feat tembl:eclac\* -sbegin 51 -send 100 -out test.out -osf embl -auto FI test.out FZ = 7381 FP 5 /^ID / FP 5 /^FH / FP /^ +ggaagagagt caattcaggg tggtgaatgt gaaaccagta acgttatacg +50/ FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/ FP /^FT CDS 29..>50\n/ FP /^FT CDS <1..>50\n/ // ID featseqset-rev-embl AQ seqretset CL -feat tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -osf embl -auto FI test.out FZ = 7525 FP 5 /^ID / FP 5 /^FH / FP /^ +cgtataacgt tactggtttc acattcacca ccctgaattg actctcttcc +50\n/ FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/ FP /^FT CDS complement[(]<1..22[)]\n/ FP /^FT CDS complement[(]<1..>50[)]\n/ // ID featseqset-end-msf AQ seqretset CL -feat tembl:eclac\* -send 100 -out test.out -osf msf -auto FI test.out FZ = 1107 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 4203/ FP / +Name: ECLACI .* Check: 8066/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4450 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t79\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t31\t100\t0[.]000\t[+]\t[.].*FeatFlags "0x2"/ // ID featseqset-begin-msf AQ seqretset CL -feat tembl:eclac\* -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 1328/ FP / +Name: ECLACI .* Check: 2937/ FP /^ECLAC ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^ECLACI cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t29\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x2" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[+]\t[.].*FeatFlags "0x3"/ // ID featseqset-rev-msf AQ seqretset CL -feat tembl:eclac\* -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: ECLAC .* Check: 2885/ FP / +Name: ECLACI .* Check: 9768/ FP /^ECLAC cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ECLACI ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 4089 FP 5 /^##Type DNA/ FP /^ECLAC\tEMBL\tCDS\t1\t22\t0[.]000\t[-]\t[.].*FeatFlags "0x1" .*gene "lacI"/ FP /^ECLACI\tEMBL\tCDS\t1\t50\t0[.]000\t[-]\t[.].*FeatFlags "0x3"/ // ########################################################### # seqret (sequence and feature input) associated qualifiers ########################################################### ID showalign-ex AP showalign IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FZ = 2235 FP /^HBB_HUMAN --------VHLTPE\.K\.AVTALWG\.VN-VD\.V\.GEA\.GR-LLVvY\.WTQR\.\.ES\.GD\.ST\n/ FP /^Consensus xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx\n/ // ID showalign-ex2 UC Show non-identities between the sequences AP showalign CL -show=n IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex3 UC Show all of the sequences AP showalign CL -show=a IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex4 UC Show identities between the sequences AP showalign CL -show=i IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex5 UC Show similarities between the sequences AP showalign CL -show=s IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex6 UC Show dissimilarities between the sequences AP showalign CL -show=d IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex7 UC Use the first sequence as the reference to compare to: AP showalign CL -ref=1 IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex8 UC Show a range of sequences in uppercase, everything else in lowercase AP showalign CL -nocon -ref=1 -sl -upper 9-15 -nosimilarcase IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex9 UC Display the sequences in alphabetic order: AP showalign CL -order=a IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex10 UC Display the sequences in order of similarity to the reference sequence AP showalign CL -order=s IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex11 UC Format for HTML and highlight some interesting regions in different colours: AP showalign CL -html -high '4-13 green 43-43 red 51-56 blue' IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex12 UC No consensus line at the bottom UC No ruler line UC No numbers line UC Don't repeat the reference sequence at the bottom of the sequences UC Use sequence 1 as the reference sequence UC Display residues from position 10 to 30 only AP showalign CL -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30 IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showdb-ex UC Display information on the currently available databases: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+P\s+OK\s+OK\s+OK/ FP /^tembl\s+N\s+OK\s+OK\s+OK/ // ID showdb-ex2 UC Write the results to a file: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -outfile showdb.out FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI showdb.out FP /^tsw\s+P\s+OK\s+OK\s+OK/ FP /^tembl\s+N\s+OK\s+OK\s+OK/ // ID showdb-ex3 UC Display information on one explicit database: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -database tsw FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+P\s+OK\s+OK\s+OK/ FP 0 /^tembl/ // ID showdb-ex4 UC Display information on the databases formatted in HTML: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tswPOK/ FP /^temblNOK/ // ID showdb-ex5 UC Display protein databases only: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -nonucleic FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+P\s+OK\s+OK\s+OK/ FP 0 /^[^#]\S*\s+N/ // ID showdb-ex6 UC Display the information with no headings: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -noheading FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /\A\S+\s+[PN]\s+/ FP 0 /\A#/ // ID showdb-ex7 UC Display just a list of the available database names: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -noheading -notype -noid -noquery -noall -nocomment -auto FI stdout FP /^tsw\s+\n/ FP /^tembl\s+\n/ // ID showdb-ex8 UC Display only the names and types: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -only -type FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+P\s+\n/ FP /^tembl\s+N\s+\n/ // ID showfeat-ex AP showfeat IN tembl:hsfau1 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau1.showfeat FZ = 1429 FP /\|=+\| 2016\n/ FP 5 / mRNA\n/ FP /-> source\n/ // ID showfeat-ex2 UC Display 'joined' features on one line with positions: AP showfeat CL -sort join -pos IN tembl:hsfau1 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau1.showfeat FZ = 1150 FP /\|=+\| 2016\n/ FP /mRNA\n/ FP /source\n/ // ID showfeat-ex3 UC Display just positions and names of CDS features - this can be used as a regions file in showseq: AP showfeat CL -matchtype CDS -width 0 -noid -nodesc -noscale -pos IN tembl:hsfau1 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau1.showfeat FZ = 54 FP /CDS/ // ID showorf-ex AP showorf IN tembl:paamir IN IN FI stderr FC = 10 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showorf FZ = 22690 FP /^F1 +1 G T A G R A S A R S P P A G R R E 17\n/ FP /^R2 +106 Y R Q G L M Q E I V V L R A V P 91\n/ // ID showseq-ex AP showseq CL tembl:paamir -sbeg 1 -send 100 IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 793 FP 2 /^\s+\|=+\|\n\s+promoter note="/ OC Note that although we asked for the sequence display to end at OC position '100', it has displayed the sequence up to the end of the line OC - position '120'. This is a feature of this program to make the display OC of things like restriction enzyme cutting sites easier. // ID showseq-ex2 UC The standard list of output formats are only a small selection of the UC possible ways in which a sequence might be displayed. Precise control UC over the output format is acheived by selecting the qualifier '-format 0' UC (Option 0 in the list of things to display). For example, UC by choosing format '0' and then specifying that we want to display the UC things: 'b,s,t,c', we will output the sequence in the following way: AP showseq CL tembl:paamir -sbeg 1 -send 120 IN 0 IN b,s,t,c IN FI stderr FC = 28 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 511 FP /^ ggtacc/ // ID showseq-ex3 UC Display only the sequence: AP showseq CL tembl:paamir -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 143 FP /^ ggtacc/ // ID showseq-ex4 UC Protein sequence can be displayed in three-letter codes. (The codes are displayed downwards, so the first code is 'Met'): AP showseq CL tsw:rs24_fugru -three -format 2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rs24_fugru.showseq FZ = 990 FP /^ MAATVT/ // ID showseq-ex5 UC Number the sequence lines in the margin: AP showseq CL tembl:paamir -sbeg 1 -send 100 -format 1 -number IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 232 FP /^ 1 ggtacc/ // ID showseq-ex6 UC Start the numbering at a specified value ('123' in this case): AP showseq CL tembl:paamir -sbeg 1 -send 100 -format 1 -number -offset 123 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 233 FP /^ 123 ggtacc/ // ID showseq-ex7 UC Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase). AP showseq CL tembl:paamir -sbeg 1 -send 100 -format 1 -slower -upper '25-45,101-203,333-362' IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 225 FP /tgctCGAT/ // ID showseq-ex8 UC Translate selected regions: AP showseq CL tembl:paamir -sbeg 1 -send 120 -format 4 -trans 25-49,66-76 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 937 FP /R S P P A G R R V/ // ID showseq-ex9 UC Add your own annotation to the display: AP showseq CL tembl:paamir -sbeg 1 -send 100 -format 2 -send 120 -annotation '13-26 binding site 15-15 SNP' IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.showseq FZ = 919 FP /binding site/ // ID shuffleseq-ex UC This makes two randomised copies of the input sequence: AP shuffleseq CL -shuffle 2 IN tembl:mmam IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## ## hard to test - randomised but same length ## FI mmam.fasta FZ = 946 FP /^>MMAM/ // # fix output file in example ID sigcleave-ex AP sigcleave IN tsw:ach2_drome IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ach2_drome.sig FP /^[(]1[)] Score 13\.739 length 13 at residues 29->41\n/ FP /^ Sequence: LLVLLLLCETVQA\n/ FP 9 /^ Sequence: / // ID sigcleave-multi AP sigcleave IN tsw:a* IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI act1_fugru.sig FP /^[(]1[)] Score 13\.739 length 13 at residues 29->41\n/ FP /^ Sequence: LLVLLLLCETVQA\n/ FP 25 /^ Sequence: / FP 2 /^# No scores over 3.50\n/ FP 12 /^# Reporting scores over 3.50\n/ FP 12 /^# Sequence: / // ID silent-ex PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA AP silent IN tembl:hsfau IN ecori,hindiii IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.silent FZ = 885 FP /^ +272 +267 Rev +HindIII +AAGCTT +268 +A.A +Yes +A->T\n/ // ID silent-seqs PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA AP silent CL -sshow -tshow IN tembl:hsfau IN ecori,hindiii IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.silent FZ = 2701 FP /^ +272 +267 Rev +HindIII +AAGCTT +268 +A.A +Yes +A->T\n/ FP /^\n/ // ID sixpack-ex AP sixpack IN tembl:paamir IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.sixpack FZ = 25535 FP /^ P P A W A G D R S H E R Q L A A R Q P A F1\n/ FP /^ R Q H G R G T A P M S A N S L L G S L R F2\n/ FP /^ A S M G G G P L P [*] A P T R C S A A C A F3\n/ FP /^ 1261 ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg 1320\n/ FI paamir.fasta FZ = 9444 FP /^>PAAMIR_2_ORF4 Translation of PAAMIR in frame 2, ORF 4, threshold 1, 210aa\n/ FP /^PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP\n/ FP 67 /^>/ // ID sixpack-mstart AP sixpack CL -mstart IN tembl:paamir IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.sixpack FZ = 25535 FP /^ P P A W A G D R S H E R Q L A A R Q P A F1\n/ FP /^ R Q H G R G T A P M S A N S L L G S L R F2\n/ FP /^ A S M G G G P L P [*] A P T R C S A A C A F3\n/ FP /^ 1261 ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg 1320\n/ FI paamir.fasta FZ = 4506 FP /^>PAAMIR_2_ORF2 Translation of PAAMIR in frame 2, ORF 2, threshold 1, 196aa\n/ FP /^MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSI\n/ FP 30 /^>/ // ID sirna-ex AP sirna IN tembl:hsfau IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.sirna FZ = 7238 FP /GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT/ FI hsfau.fasta FZ = 6035 FP /aaaagtgagaggtcagactccta/ // ID sirna-ex2 UC Show the first two bases of the 23 base target region in brackets. These do not form part of the sequence to be ordered, but it is useful to see if the 23 base region starts with an 'AA'. AP sirna CL -context IN tembl:hsfau IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.sirna FZ = 7721 FP /\(AA\)GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT/ FI hsfau.fasta FZ = 6035 FP /aaaagtgagaggtcagactccta/ // ID skipseq-ex UC This does not skip any sequences. It is exactly equivalent to seqret: AP skipseq IN tembl:eclac* IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.fasta FZ = 15618 FP 5 /^>/ // ID skipseq-ex2 UC This skips the first input sequence, writing out the others: AP skipseq CL -skip 1 IN tembl:eclac* IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.fasta FZ = 7940 FP 4 /^>/ // ID splitter-ex UC Split a sequence into sub-sequences of 10,000 bases (the default size) with no overlap between the sub-sequences: AP splitter CL tembl:AP000504 ap000504.split FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ap000504.split FZ = 102677 FP /\A>AP000504_1-10000/ FP /^>AP000504_10001-20000/ FP /^>AP000504_90001-100000/ FP 10 /^>/ // ID splitter-ex2 UC Split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence: AP splitter CL tembl:AP000504 ap000504.split -size=50000 -over=3000 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ap000504.split FZ = 108068 FP /\A>AP000504_1-50000/ FP /^>AP000504_47001-97000/ FP 3 /^>/ // # update example ID stretcher-ex AP stretcher CL tsw:hba_human tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.stretcher FZ > 1442 FP /^# Matrix: EBLOSUM62\n/ FP /^# Gap_penalty: 12\n/ FP /^# Extend_penalty: 2\n/ FP /^# Identity: +64/148 \(43\.2%\)\n/ FP /^# Score: 272\n/ FP /^HBA_HU V-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DL\n/ FP /^HBB_HU VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDL\n/ // ID stssearch-ex AP stssearch IN tembl:eclac* IN ../../data/lac.primers IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.stssearch FZ = 710 FP /^ECLAC: PrimA PrimerA matched at 532\n/ FP /^ECLAC: \(rev\) PrimA PrimerB matched at 689\n/ // ID supermatcher-ex TI 400 AP supermatcher CL tembl:ec* tembl:eclac -word 50 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI eclac.supermatcher FZ > 71230 FP /^ECLAC +1 / FP /^# Score: 37385\.0/ FP 5 /^# Score: / FP /^ECLACA +1801 [acgt]+ +1832\n/ // ID supermatcher-range TI 400 AP supermatcher CL tembl:ec* tembl:eclac -word 50 -sbegin2 101 -send2 -101 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI eclac.supermatcher FZ > 69555 FP /^ECLAC +101 / FP /^# Score: 36385\.0/ FP 5 /^# Score: / FP /^ECLACA +1701 [acgt]+ +1732\n/ // ID syco-ex AP syco CL -plot -cfile Epseae.cut IN tembl:paamir IN ps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 16 FP /^Created syco.ps\n/ FI paamir.syco FZ = 0 FI syco.ps FZ = 62558 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID tcode-ex AP tcode IN tembl:hsfau1 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau1.tcode FZ = 21691 FP /^ 1 200 0.673 Non-coding/ FP /^ 22 221 0.767 No opinion/ FP /^ 37 236 0.951 Coding/ // ID tcode-ex2 UC Produce a graphical plot CL -plot -graph cps AP tcode IN tembl:hsfau1 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 17 FP /^Created tcode.ps\n/ FI tcode.ps FP /^%%Title: PLplot Graph/ FI hsfau1.tcode FZ = 0 // ID textsearch-ex UC Search for 'lactose': AP textsearch CL tsw:* 'lactose' IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 100k_rat.textsearch FZ = 169 FP /^tsw-id:LACI_ECOLI LACI_ECOLI P03023\s+LACTOSE OPERON REPRESSOR/ FP /^tsw-id:LACY_ECOLI LACY_ECOLI P02920\s+LACTOSE PERMEASE/ // ID textsearch-ex2 UC Search for 'lactose' or 'permease' in E.coli proteins: AP textsearch CL tsw:*_ecoli 'lactose | permease' IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.textsearch FZ = 180 FP /^tsw-id:LACI_ECOLI LACI_ECOLI P03023\s+LACTOSE OPERON REPRESSOR/ FP /^tsw-id:LACY_ECOLI LACY_ECOLI P02920\s+LACTOSE PERMEASE/ // # update example ID textsearch-ex3 UC Output a search for 'lacz' formatted with HTML to a file: AP textsearch CL tembl:* 'lacz' -html -outfile embl.lacz.html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI embl.lacz.html FZ = 349 FP /^tembl-id:ECLACECLACJ01636\s+E.coli lactose operon with lacI, lacZ, lacY and lacA genes./ // ID tfextract-keep ## Note: yeast is now fungi rather than plant. DL keep AP tfextract PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/site.dat FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI tffungi FZ = 121 FP /^Y\$ADH1_02/ FI tfinsect FZ = 0 FI tfvertebrate FZ = 676 FC = 7 FP /^HS\$ALBU_01 +tGGTTAGtaattactaa R00077 T01951; HNF-1C;Quality: 1; Species: human, Homo sapiens./ FP 5 /^HS\$ALBU/ FP 2 /^MOUSE/ FI tfplant FZ = 0 FI tfother FZ = 0 // ID tfm-ex AP tfm CC wossname documentation subject to updates - will break file size test CC On some systems 'more' also reports the filename at the start of the output CL wossname FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ > 43000 FP 1 /^ +Finds programs by keywords in their one-line documentation\n/ FP 2 /^ +-explode/ // ID tfscan-ex CC Needs tfextract to reformat TRANSFAC data AP tfscan PP EMBOSS_DATA=../tfextract-keep/ PP export EMBOSS_DATA IN tembl:hsfos IN v IN IN FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfos.tfscan FZ = 623 FC = 13 FP /^MOUSE\$FCGR3A_02 R04413 3287 3292 ttcctc\n/ FP /^ +T00702; PU.1;Quality: 3; Species: mouse, Mus musculus.\n/ // ID tmap-ex AP tmap CL tsw:opsd_human -out tmap.res -graph cps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 16 FP /^Created tmap.ps\n/ FI tmap.res FZ = 1432 FP 2 /^ 43 69 1 YMFLLIVLGFPINFLTLYVTVQHKKLR\n/ FI tmap.ps FZ = 39837 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID tranalign-ex AP tranalign CL ../../data/tranalign.seq ../../data/tranalign.pep tranalign2.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI tranalign2.seq FZ = 2375 FP /^>HSFAU1/ FP /^cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg/ // # update the examples ID transeq-ex UC To translate a sequence in the first frame (starting at the first base and proceeding to the end): AP transeq CL tembl:paamir amir.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 821 FP /^>PAAMIR_1/ FP /^GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR\*SACCSP\n/ // ID transeq-ex2 UC To translate a sequence in the second frame: AP transeq CL tembl:paamir amir.pep -frame=2 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 820 FP /^>PAAMIR_2/ FP /^VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR\*ATVTGEETDGIAPGAAADRPAVLR\n/ // ID transeq-ex3 UC To translate a sequence in the first frame in the reverse sense (starting at the last frame 1 codon and proceeding to the start): AP transeq CL tembl:paamir amir.pep -frame=-1 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 820 FP /^>PAAMIR_4/ FP /^SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS\*AIFRIGSRRFIAS\n/ // ID transeq-ex4 UC To translate a sequence in all three forward frames: AP transeq CL tembl:paamir amir.pep -frame=F FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 2460 FP /^>PAAMIR_1/ FP /^>PAAMIR_2/ FP /^>PAAMIR_3/ FP /^CWARSAVGRWR\*STSWSAC\*APASRST\*SFPQQPGRAR\*RPER\*PCYSLLPICGWPPTSS\n/ // ID transeq-ex5 UC To translate a sequence in all three reverse frames: AP transeq CL tembl:paamir amir.pep -frame=R FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 2461 FP /^>PAAMIR_4/ FP /^>PAAMIR_5/ FP /^SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS\*AIFRIGSRRFIAS\n/ FP /^LEELVGGHPQIGKSE\*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA\n/ FP /^>PAAMIR_6/ // ID transeq-ex6 UC To translate a sequence in all six forward and reverse frames: AP transeq CL tembl:paamir amir.pep -frame=6 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 4921 FP /^>PAAMIR_1/ FP /^>PAAMIR_2/ FP /^>PAAMIR_3/ FP /^>PAAMIR_4/ FP /^>PAAMIR_5/ FP /^>PAAMIR_6/ FP /^LEELVGGHPQIGKSE\*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA\n/ // ID transeq-ex7 UC To translate a specific set of regions corresponding to a known set of coding sequences: AP transeq CL tembl:paamir amir.pep -reg=2-45,67-201,328-509 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 209 FP /^>PAAMIR_1/ FP /^VRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAE\n/ FP /^X\Z/ // ID transeq-ex8 UC To translate a mitochondrial sequence using the mammalian mitochondrion genetic code table: AP transeq CL ../../data/mito.seq mito.pep -table 2 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mito.pep FZ = 5626 FP /^>NC_001321.1_1/ FP /^VNY\*SAHDHNMTEVSYIWYFFIFFGGLARTPLWP\*\*VSSQSDKL\*LGLDVFVIWLAQPTC\n/ // ID transeq-list1 UC To translate from a list of sequences and test the ranges are set correctly AP transeq CL @../../data/range1.list list.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI list.pep FZ = 733 FP /^AAGKKLPR\n/ FP /^STVTQLPTKWWPSRTSLLVRSSTPEETRPSRLTC\*PMAAASVPLSPAAHPLASTRRLSSV\n/ FP /^KKKKX\n/ // ID transeq-list2 UC To translate from a list of sequences and test the ranges are set correctly AP transeq CL @../../data/range2.list list.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI list.pep FZ = 1135 FP /^PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSLIAERQRVMAVQVALRR\n/ FP /^LFSVVAAVPEIKMLLMTEKKKKKX\n/ FP /^MVAIKDITARQILDSRGNPTVEVDLLTDGGCFRAAVPSGASTGIYEALELRDKDQTKFMG\n/ FP /^QLMRIEESLGSDCQYAGAGFRHPN\*\n/ // ID transeq-list12 UC To translate from a list of sequences and test the ranges are set correctly AP transeq CL @../../data/range12.list list.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI list.pep FZ = 631 FP /^AAGKKLPR\n/ FP /^MVAIKDITARQILDSRGNPTVEVDLLTDGGCFRAAVPSGASTGIYEALELRDKDQTKFMG\n/ FP /^QLMRIEESLGSDCQYAGAGFRHPN\*\n/ // ID trimest-ex AP trimest CL tembl:hsfau hsfau.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 574 FP /poly-A tail removed/ // # madness - never trims anything ID trimseq-ex AP trimseq CL tembl:hsfau hsfau.seq -window 1 -percent 100 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 562 FP /^>HSFAU / // ID trimseq-ex2 AP trimseq CL tembl:hsfau hsfau.seq -window 5 -percent 40 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 562 FP /^>HSFAU / // ID trimseq-ex3 AP trimseq CL tembl:hsfau hsfau.seq -window 20 -percent 80 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 562 FP /^>HSFAU / // ID trimseq-ex4 AP trimseq CL tembl:hsfau hsfau.seq -window 20 -percent 10 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 562 FP /^>HSFAU / // ID trimseq-ex5 AP trimseq CL tembl:hsfau hsfau.seq -window 20 -percent 50 -strict FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 562 FP /^>HSFAU / // ID trimseq-ex6 AP trimseq CL tembl:hsfau hsfau.seq -window 1 -percent 100 -star FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 562 FP /^>HSFAU / // ID trimseq-ex7 AP trimseq CL tembl:hsfau hsfau.seq -window 20 -percent 50 -noright FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.seq FZ = 562 FP /^>HSFAU / // ID twofeat-ex UC Without the -twoout option the output report contains just one feature for every pair of features found. AP twofeat CL tembl:hsfau IN polyA_signal IN polyA_site IN 10 IN 50 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.twofeat FZ = 516 FP /484 509 0.000 484 489 509 509/ // ID twofeat-ex2 UC The -twoout option makes the output report give the pairs of features found. The ouput report format type has been changed to display the full original pairs of faetures in GFF format. AP twofeat CL -twoout -rformat gff tembl:hsfau IN polyA_signal IN polyA_site IN 10 IN 50 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau.twofeat FZ = 192 FP /polyA_signal/ // ID union-ex UC the file 'cds.list' contains a list of the regions making up the coding sequence of 'embl:hsfau': AP union IN @../../data/cds.list IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfau1.fasta FZ = 447 FP 1 /^>/ // ID vectorstrip-ex AP vectorstrip CL @../../data/vecseqs.list IN IN ../../data/vectors IN IN IN vector.strip IN vector.fasta FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI vector.strip FZ = 1835 FP /tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca/ FI vector.fasta FZ = 457 FP /tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca/ // ID water-ex AP water CL tsw:hba_human tsw:hbb_human IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.water FZ > 1175 FP /^# Score: 293.5\n/ FP /^HBA_HUMAN +2 +LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS- +49\n/ FP /^HBB_HUMAN +3 +LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST +50\n/ FP /^HBA_HUMAN +50 +----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP +95\n/ FP /^# Identity: +63/145 \(43\.4%\)\n/ FP /^# Similarity: +88/145 \(60.7%\)\n/ // ID whichdb-ex AP whichdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME TI 300 CL -showall IN hsfau1 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.whichdb FZ > 0 FP /^tembl:hsfau1\n/ // ID wobble-ex UC Here is a sample session with wobble. The example sequence is from Pseudomonas aeruginosa, which has a high G+C content and a very biased third codon position (if it can be G or C, it usually is). AP wobble IN tembl:paamir IN cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 18 FP /^Created wobble.ps\n/ FI paamir.wobble FZ = 46 FP /^Expected GC content in third position = 66.54\n/ FI wobble.ps FZ = 110240 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID wordcount-ex AP wordcount CL tembl:rnu68037 -wordsize=3 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rnu68037.wordcount FZ = 432 FP /\Actg\s+54\n/ FP /^aaa\s+1\Z/ // ID wordmatch-ex AP wordmatch CL tsw:hba_human tsw:hbb_human IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP /^ +5 HBA_HUMAN +[+] +58\.\.62 +HBB_HUMAN +[+] +63\.\.67\n/ FP /^ +4 HBA_HUMAN +[+] +14\.\.17 +HBB_HUMAN +[+] +15\.\.18\n/ FP /^ +4 HBA_HUMAN +[+] +116\.\.119 +HBB_HUMAN +[+] +121\.\.124\n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID wossname-ex UC Search for programs with 'restrict' in their description: AP wossname CL restrict FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^recoder / FP /^remap / FP /^restover / FP /^silent / FP 0 /seqret / // ID wossname-ex2 UC Display a listing of programs in their groups: AP wossname CL -search '' FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^recoder / FP /^remap / FP /^restover / FP /^silent / FP /^seqret / FP /^INFORMATION/ // ID wossname-ex3 UC Display an alphabetic listing of all programs: AP wossname CL -search '' -alphabetic FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP s /\AALPHABETIC.*\naaindexextract / // ID wossname-ex4 UC Display only the groups that the programs can belong to: AP wossname CL -search '' -groups FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^[A-Z]/ FP 0 /^[^A-Z]/ // ID wossname-ex5 UC Output html tags around the list of program groups: AP wossname CL -groups -html -prelink '#' IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^
  • ALIGNMENT CONSENSUS
    • \n/ // ID wossname-ex6 UC Output html tags around the list of programs: AP wossname CL '' -html -prelink CL 'http://emboss.sf.net/apps/' CL -postlink '.html' -out wossname.html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI wossname.html FP /AFULL \.\.\nAACCGG\n/ FP 1 /^>BFULL \.\.\nAACGGG\n/ FC = 32 // ID align-matcher-markx10 AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 CL -aformat markx10 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^>AFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nAACCGG\n/ FP 1 /^>BFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nAACGGG\n/ FC = 53 // ID align-matcher-fasta AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 CL -aformat fasta IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^>AFULL\n/ FP 1 /^AACCGG\n/ FP 1 /^>BFULL\n/ FP 1 /^AACGGG\n/ FC = 4 // ID align-matcher-msf AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 CL -aformat msf IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^AFULL +AACCGG\n/ FP 1 /^BFULL +AACGGG\n/ FC = 13 // ID align-matcher-msfall AP matcher CL -gapopen 5 -gapextend 1 -stdout CL -aformat msf IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^AFULL +AAACCCGGG\.\.TTT\n/ FP 1 /^BFULL +AAAC\.\.GGGCCTTT\n/ FC = 13 // ID align-matcherprot-full AP matcher CL -stdout IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +198\n/ FP 1 /^ 60 70\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: . :::::.:.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 40 // ID align-matcherprot-begin AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +195\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: . :::::.:.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 40 // ID align-matcherprot-end AP matcher CL -stdout -send1 15 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/13 \(61\.5%\)/ FP /^# Score: +42\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL FIAAEEFLFIIAA\n/ FP 1 /^ ::::..: .:::\n/ FP 1 /^ BFULL FIAADDFFILIAA\n/ FP 1 /^ 10 \n/ FC = 34 // ID align-matcherprot-begin2 AP matcher CL -stdout -sbegin2 5 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +36\/64 \(56\.2%\)/ FP /^# Score: +180\n/ FP 1 /^ AFULL IAALEEFFIIAEFL\n/ FP 1 /^ ::: . :::::.:.\n/ FP 1 /^ BFULL IAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 40 // ID align-matcherprot-end2 AP matcher CL -stdout -send2 -3 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +198\n/ FP 1 /^ 60 70\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: . :::::.:.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 40 // ID align-matcherprot-begendall AP matcher CL -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/11 \(54\.5%\)/ FP /^# Score: +32\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL AAEEFLFIIAA\n/ FP 1 /^ BFULL AADDFFILIAA\n/ FP 1 /^ 10 \n/ FC = 34 // ID align-wordmatch-same AP wordmatch CL tembl:eclaci tembl:eclaci -word 50 -auto FI eclaci.wordmatch FC = 18 FP /^ +1113 +ECLACI +[+] +1\.\.1113 +ECLACI +[+] +1\.\.1113\n/ FI ECLACI.gff FZ = 137 FP /^ECLACI\twordmatch\tmisc_feature\t1\t1113\t1\.000\t/ // ID align-wordmatch-pair AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat pair IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HUMAN 58 HGKKV 62\n/ FP 1 /^ \|\|\|\|\|\n/ FP 2 /^ \|\|\|\|\n/ FP 1 /^HBB_HUMAN 63 HGKKV 67\n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID align-wordmatch-srspair AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat srspair IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HUMAN 58 HGKKV 62\n/ FP 1 /^ \|\|\|\|\|\n/ FP 2 /^ \|\|\|\|\n/ FP 1 /^HBB_HUMAN 63 HGKKV 67\n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID align-wordmatch-markx0 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx0 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HU HGKKV\n/ FP 1 /^ :::::\n/ FP 1 /^HBB_HU HGKKV\n/ FP 1 /^ 60 \n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID align-wordmatch-markx1 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx1 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HU HGKKV\n/ ## found for numbering and for alignment in first hit FP 2 /^ \n/ FP 1 /^HBB_HU HGKKV\n/ FP 1 /^ 60 \n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID align-wordmatch-markx2 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx2 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^ 60 \n/ FP 1 /^HBA_HU HGKKV\n/ FP 1 /^HBB_HU \.HLTP\n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID align-wordmatch-markx3 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx3 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^>HBA_HUMAN \.\.\nHGKKV\n/ FP 1 /^>HBB_HUMAN \.\.\nHGKKV\n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID align-wordmatch-markx10 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx10 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 3 /^>HBA_HUMAN \.\.\n/ FP 3 /^; sq_len: 141\n/ FP 1 /^; al_start: 58\n/ FP 1 /^; al_stop: 62\n/ FP 1 /^; al_display_start: 58\n/ FP 2 /^HGKKV\n/ FP 3 /^>HBB_HUMAN \.\.\n/ FP 3 /^; sq_len: 146\n/ FP 1 /^; al_start: 63\n/ FP 1 /^; al_stop: 67\n/ FP 1 /^; al_display_start: 63\n/ FI HBA_HUMAN.gff FZ = 336 FP /^HBA_HUMAN\twordmatch\tmisc_feature\t58\t62\t1\.000\t/ FI HBB_HUMAN.gff FZ = 336 FP /^HBB_HUMAN\twordmatch\tmisc_feature\t63\t67\t1\.000\t/ // ID align-merger-fasta AP merger CL -aformat fasta IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 108 FP /accggaaaaaaga\n[-]+\n/ FP /^---------------------gtgaatgaagtcgcttaagcaatcaatgtcggatgcggc\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx0 AP merger CL -aformat markx0 IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 417 FP /^# Score: 795\.0\n/ FP / 1340 1350\nECLACY cgctt/ FP /^ECLACY cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^ECLACA [-]+gtgaatgaa\n +\n/ FP /^ECLACA .*tccgaccaac\n 10/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx1 AP merger CL -aformat markx1 IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 417 FP /^# Score: 795\.0\n/ FP / 1340 1350\nECLACY cgctt/ FP /^ECLACY cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^ECLACA [-]+gtgaatgaa\n +\n/ FP /^ECLACA .*tccgaccaac\n 10/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx2 AP merger CL -aformat markx2 IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 289 FP /^# Score: 795\.0\n/ FP / 1340 1350\nECLACY cgctt/ FP /^ECLACY cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^ECLACY [acgt]+gtgaatgaa\nECLACA [-]+\.\.\.\.\.\.\.\.\.\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx3 AP merger CL -aformat markx3 IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 163 FP /^# Score: 795\.0\n/ FP /^cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^-----------------------------------------gtgaatgaa\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx10 AP merger CL -aformat markx10 IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 184 FP /^; sw_score: 795.0\n/ FP /^cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^-----------------------------------------gtgaatgaa\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-match AP merger CL -aformat match IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 26 FP /^ 159 ECLACY +[+] +1342\.\.1500 ECLACA +[+] +1\.\.159\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-msf AP merger CL -af msf IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 265 FP /^ECLACY +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^ECLACA +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gtgaatgaa\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-pair AP merger CL -aformat pair IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FZ > 1445 FP /^# Score: 795\.0\n/ FP /^ECLACY +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^ECLACA +1 [-]+gtgaatgaa +9\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-score AP merger CL -aformat score IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 9 FP 0 /^# Score:/ FP /^ECLACY ECLACA 3173 \(795\.0\)\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-simple AP merger CL -aformat simple IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 289 FP /^# Score: 795\.0\n/ FP /^ECLACY +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^ECLACA +1 [-]+gtgaatgaa +9\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-srs AP merger CL -aformat srs IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 225 FP /^# Score: 795\.0\n/ FP /^ECLACY +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^ECLACA +1 [-]+gtgaatgaa +9\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-srspair AP merger CL -aformat srspair IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 289 FP /^# Score: 795\.0\n/ FP /^ECLACY +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^ECLACA +1 [-]+gtgaatgaa +9\n/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-tcoffee AP merger CL -aformat tcoffee IN tembl:eclacy IN tembl:eclaca IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacy.merger FC = 167 FP /^2\nECLACY 1500 ttccagct/ FP /^! score=795.0\n/ FP /^1342 1 0 1 0\n/ FP /^1500 159 0 1 0\n/ FP 0 /^1501/ FI eclacy.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-needle-full AP needle CL -gapopen 16 -gapext 4 -stdout IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/64 \(12\.5%\)/ FP /^# Score: +24\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg 50\n/ FP 1 /^ + \|\|\|\|\.\.\|\.\.\|\|\| \n/ FP 1 /^BFULL +1 ------------aaacgggccttt-------------------------- 12\n/ FC = 36 // ID align-needle-part AP needle CL -gapopen 16 -gapext 4 -stdout IN ../../data/aligna.dna IN ../../data/alignapart.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +46\/67 \(68\.7%\)/ FP /^# Score: +162\.0\n/ FP 1 /^AFULL 48 ttgggccaattggcatg 64\n/ FP 1 /^ \|\| \.\.\|\|\.\.\|\| \n/ FP 1 /^APART 47 tt-aaccggtt------ 56\n/ FC = 36 // ID align-needle-begin AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/60 \(13\.3%\)/ FP /^# Score: +24\.0\n/ FP 1 /^AFULL +5 aaccggttaaacccgggtttaaaaccccggggttttcccaaatttgggcc 54\n/ FP 1 /^ + \|\|\|\|\.\.\|\.\.\|\|\| +\n/ FP 1 /^BFULL +1 --------aaacgggccttt------------------------------ 12\n/ FC = 36 // ID align-needle-end AP needle CL -gapopen 16 -gapext 4 -stdout -send1 15 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +3\/24 \(12\.5%\)/ FP /^# Score: +15\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaa--------- 15\n/ FP 1 /^BFULL +1 ------------aaacgggccttt 12\n/ FC = 32 // ID align-needle-begin2 AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin2 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/64 \( 9\.4%\)/ FP /^# Score: +22\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg 50\n/ FP 1 /^BFULL +5 --------------------------------gggccttt---------- 12\n/ FC = 36 // ID align-needle-end2 AP needle CL -gapopen 16 -gapext 4 -stdout -send2 -3 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/64 \( 9\.4%\)/ FP /^# Score: +14\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg 50\n/ FP 1 /^BFULL +1 ------------aaacgggcct---------------------------- 10\n/ FC = 36 // ID align-needle-begendall AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/11 \(45\.5%\)/ FP /^# Score: +21\.0\n/ FP 1 /^AFULL +5 aaccggttaaa 15\n/ FP 1 /^BFULL +2 aacggg----- 7\n/ FC = 32 // ID align-water-full AP water CL -gapopen 5 -gapext 1 -stdout IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\.0\n/ FP 1 /^AFULL 13 aaacccggg--ttt 24\n/ FP 1 /^BFULL 1 aaa--cgggccttt 12\n/ FC = 32 // ID align-water-part AP water CL -gapopen 5 -gapext 1 -stdout IN ../../data/aligna.dna IN ../../data/alignapart.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +46\/62 \(74\.2%\)/ FP /^# Score: +196\.0\n/ FP 1 /^AFULL +5 aaccggttaaacccgggtttaaaaccccggggtttt---cccaaatttgg 51\n/ FP 1 /^APART +1 aaccggttaaacccgggtttaaaaccccggggttttaaaccc------gg 44\n/ FC = 36 // ID align-water-begin AP water CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\.0\n/ FP 1 /^AFULL 13 aaacccggg--ttt 24\n/ FP 1 /^BFULL 1 aaa--cgggccttt 12\n/ FC = 32 // ID align-water-end AP water CL -gapopen 5 -gapext 1 -stdout -send1 15 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/10 \(70\.0%\)/ FP /^# Score: +25\.0\n/ FP 1 /^AFULL 5 aaccgg--tt 12\n/ FP 1 /^BFULL 2 aacgggcctt 11\n/ FC = 32 // ID align-water-begin2 AP water CL -gapopen 5 -gapext 1 -stdout -sbegin2 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/9 \(77\.8%\)/ FP /^# Score: +29\.0\n/ FP 1 /^AFULL 50 gggccaatt 58\n/ FP 1 /^BFULL 5 gggcc--tt 11\n/ FC = 32 // ID align-water-end2 AP water CL -gapopen 5 -gapext 1 -stdout -send2 -3 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/11 \(72\.7%\)/ FP /^# Score: +30\.0\n/ FP 1 /^AFULL 44 aaatttgggcc 54\n/ FP 1 /^BFULL 1 aaa--cgggcc 9\n/ FC = 32 // ID align-water-begendall AP water CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\.0\n/ FP 1 /^AFULL 5 aaccgg 10\n/ FP 1 /^BFULL 2 aacggg 7\n/ FC = 32 // ID align-supermatcher-default TI 400 AP supermatcher CL tembl:ec* tembl:eclac -word 50 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI eclac.supermatcher FZ > 71230 FP /^ECLAC +1 / FP /^# Score: 37385\.0/ FP 5 /^# Score: / FP /^ECLACA +1801 [acgt]+ +1832\n/ // ID align-supermatcher-range TI 400 AP supermatcher CL tembl:ec* tembl:eclac -word 50 -sbegin2 101 -send2 -101 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI eclac.supermatcher FZ > 69555 FP /^ECLAC +101 / FP /^# Score: 36385\.0/ FP 5 /^# Score: / FP /^ECLACA +1701 [acgt]+ +1732\n/ // ####################################### # EMBOSS make check ####################################### ID ajtest-check AQ ajtest IN tembl:paamir IN ../../data/globins.msf IN stdout IN abc.seq IN abc.gff FI stderr FC = 4 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI kim1.out FZ = 3390 FP /^ID PAAMIR standard; DNA; UNC; 2167 BP.\n/ FI abc.seq FC = 0 FI abc.gff FC = 0 // ID ajtest-all-check AQ ajtest CL -nostdout -outfile CL -outseq outseq IN tembl:paamir IN ../../data/globins.msf IN abc.gff FI stderr FC = 4 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI kim1.out FZ = 3390 FP /^ID PAAMIR standard; DNA; UNC; 2167 BP.\n/ FI outseq FC = 0 FI abc.gff FC = 0 FI paamir.nulloutfile FC = 0 // ID complex-check AQ complex TI 300 CL -omnia IN tembl:* IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI complex.ujtable FZ = 0 FI hs989235.complex FZ = 3806 FP /^ +10 +HSHT +1658 +0[.]7314 +\n/ FI hs989235.fasta FZ = 540075 FP 44 /^>/ // ID corbatest-check AQ corbatest CC No documentation, no example CL paamir test.out FI stderr FC < 2 FP 1 /^CORBA support has not been compiled\n/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID demoalign-check AQ demoalign CC No documentation, no example CL ../../data/dna.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dna.demoalign FZ = 1212 FP 9 /^MSFM[1-3] +/ // ID demofeatures-check AQ demofeatures CC No documentation, no example IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FZ = 652 FP /\A##gff-version 2\.0\n/ FP 10 /^seq1\tdemofeature\t/ // ID demolist-check AQ demolist CC No documentation, no example CL ../../data/paamir.gff FI stderr FZ = 1083 FP 30 /^PAAMIR\tEMBL\t[^ \t]/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID demoreport-check AQ demoreport CC No documentation, no example CL tembl:paamir test.out -rformat gff FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FZ = 2043 FP 10 /^PAAMIR\tEMBL\t/ // ID demosequence-check AQ demosequence CC No documentation, no example, and no code CC Just checking it does nothing FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID demostring-check AQ demostring CC No documentation, no example IN How long is a piece of string? FI stderr FZ = 874 FP /^first token 'How'\n/ FP /^second token 'long is a piece of string[?]'\n/ FP /Warning: Unknown date/time format fred\n/ FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID demotable-check AQ demotable CC No documentation, no example IN ../../data/paamir.gff FI stderr FC = 9 FP 7 /^type [a-zA-Z_']+ found/ FP /^type 'CDS' found 2 times\n/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID entrails-check AQ entrails CL -full IN FI outfile.entrails FZ > 26000 FP /^ +taglist +string +"" +"Extra tags to report"\n/ FP /^ +ausashow +boolean +"N" +"Show the full USA in the alignment"\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID histogramtest-check AQ histogramtest CL -graph ps IN IN IN FI histogramtest.ps FZ > 0 FP /^%%/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID intconv-check AQ intconv CL stdin stdout -auto IN int main (int argc, char* argv[]) { IN int number; IN long time; IN ajint long[52]; IN ajlong int; IN exit (1); IN } FI stdout FP 4 /ajint/ FP 2 /ajlong/ FZ = 107 // ID patmattest-check AQ patmattest CC No documentation, no example IN tembl:paamir IN ACA IN FI stdout FC = 93 FP /^ACA\n15 matches found\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID prima-check AQ prima IN tembl:eclaci IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclaci.prima FZ = 1597 FP /^3 pairs found\n/ // ID primers-check RQ primer3 AQ primers CC No documentation, no example IN tembl:hsfos IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hsfos.primers FZ = 910 FP /\A\n# PRIMER3 RESULTS FOR HSFOS\n/ FP /^ 1 PRODUCT SIZE: 264\n/ FP /^ FORWARD PRIMER 2492 20 60.01 45.00 AGAATCCGAAGGGAAAGGAA\n/ FP /^ REVERSE PRIMER 2755 20 59.98 55.00 CTTCTCCTTCAGCAGGTTGG\n/ // ID seqinfo-check AQ seqinfo CC No documentation, no example IN tembl:paamir IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 163 FP /^Length:[ \t]+2167 basepairs\n/ FP /^GC Content:[ \t]+66[.]5436 %\n/ // ID seqretall-check AQ seqretall IN tembl:eclac* IN FI eclac.fasta FZ = 15618 FP 5 /^>/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID seqretallfeat-check AQ seqretallfeat CL -osf embl IN tembl:eclac* IN eclacall.embl FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclacall.embl FZ = 33282 FP 5 /^ID ECLAC/ // ID seqretset-check AQ seqretset IN tembl:eclac* IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.fasta FZ = 15618 FP 5 /^>/ // ID seqretsingle-check AQ seqretsingle IN tembl:eclac* IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eclac.fasta FZ = 7678 FP 1 /^>/ // ID testplot-check AQ testplot CC No documentation, no example CL -graph ps IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Created testplot.ps\n/ FI testplot.ps FZ > 18600 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID treetypedisplay-check AQ treetypedisplay CC No documentation, no example CL -graph ps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Created treetypedisplay.ps\n/ FI treetypedisplay.ps FZ > 9220 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID acd-calc-feat AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcfeat ../../data/feat.emft IN IN IN IN IN IN IN FI stderr FC = 2 FP 7 /:/ FP 1 /FLength \[32987\]: / FP 1 /FName: / FP 1 /FBegin \[1\]: / FP 1 /FEnd \[32987\]: / FP 1 /FProtein \[N\]:/ FP 1 /FNucleic \[Y\]: / FP 1 /FSize \[81\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-regexp AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcregexp "abc[def] ghi" IN FI stderr FC = 2 FP 1 /:/ FP 1 /Length \[12\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-seq AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcseq tembl:paamir IN IN IN IN IN IN FI stderr FC = 2 FP 6 /:/ FP 1 /Length \[2167\]: / FP 1 /Name \[PAAMIR\]: / FP 1 /Begin \[1\]: / FP 1 /End \[2167\]: / FP 1 /Protein \[N\]:/ FP 1 /Nucleic \[Y\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-seqall AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcseqall tembl:eclac* IN IN IN IN IN IN FI stderr FC = 2 FP 6 /:/ FP 1 /Length \[7477\]: / FP 1 /Name \[ECLAC\]: / FP 1 /Begin \[1\]: / FP 1 /End \[7477\]: / FP 1 /Protein \[N\]:/ FP 1 /Nucleic \[Y\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-seqset AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcseqset tembl:eclac* IN IN IN IN IN IN IN IN FI stderr FC = 2 FP 8 /:/ FP 1 /Length \[7477\]: / FP 1 /Name: / FP 1 /Begin \[1\]: / FP 1 /End \[7477\]: / FP 1 /Protein \[N\]:/ FP 1 /Nucleic \[Y\]: / FP 1 /Totweight \[5\.000\]: / FP 1 /Count \[5\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-string AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcstring "abc def" IN FI stderr FC = 2 FP 1 /:/ FP 1 /Length \[7\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ####################################### # CONSTRUCT ####################################### ID alignrunner-ex AB reconstruct AA alignrunner CC Error messages to be resolved IN ../../data/construct/ IN IN IN IN IN IN IN 10.0 IN 0.5 IN Y IN IN IN IN IN FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID contactalign-ex AB reconstruct AA contactalign CC warnings in stderr IN ../../data/construct/1hgx_a.fasta IN ../../data/construct/1hmp_a.fasta IN 10.0 IN 0.5 IN 1hgx_a_vs_1hmp_a.contactalign FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 612 FP 200 /^current position:/ // ID contactcount-ex AB reconstruct AA contactcount CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID degapseqrunner-ex AB reconstruct AA degapseqrunner CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID nawalign-ex AB reconstruct AA nawalign CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID nawalignrunner-ex AB reconstruct AA nawalignrunner CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID needlerunner-ex AB reconstruct AA needlerunner CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID scorer-ex AB reconstruct AA scorer CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID scorerrunner-ex AB reconstruct AA scorerrunner CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID substitute-ex AB reconstruct AA substitute CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID substituterunner-ex AB reconstruct AA substituterunner CC Construct test not yet defined FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ######################################################### # # EMBASSY (STRUCTURE) + scopparse (DOMAINATRIX) # ######################################################### ID pdbparse-keep AB structure DL keep TI 120 AA pdbparse IN ../../data/structure IN IN Y IN IN IN FI stdout FC = 3 FP 3 /^Processing / FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI pdbparse.log FC = 18 FP 2 /^SEQRESLENDIF/ FP 2 /^SECSTART 1 1 ILE 384\n/ FP 3 /^SECBOTH/ FP /^SECBOTH 1 1 VAL 78 ILE 81\n/ FI 1cs4.ccf FC = 537 FZ = 51353 FP 475 /^AT / FI 1ii7.ccf FC = 462 FZ = 44215 FP 402 /^AT / FI 2hhb.ccf FC = 5398 FZ = 533145 FP 4779 /^AT / // ID pdbparse-keep2 AB structure DL keep TI 120 AA pdbparse IN ../../data/structure/pdb IN IN Y IN IN IN FI stdout FC = 3 FP 3 /^Processing / FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI pdbparse.log FC = 18 FP 1 /^DUPATOMRES/ FP 5 /^BADINDEX/ FI 1fx2.ccf FC = 2399 FZ = 235421 FP 2141 /^AT / FI 4at1.ccf FC = 8134 FZ = 808387 FP 7170 /^AT / FI 1cs4.ccf FC = 6610 FZ = 654080 FP 5843 /^AT / // ID pdbplus-keep AB structure DL keep AA pdbplus RQ stride RQ naccess CC Requires stride CC Requires naccess IN ../pdbparse-keep/ IN ../../data/structure/ IN IN 3 IN 4 IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 11 FP 3 /[.]ent \>\> naccess[.]log/ FP 2 /failures: 0\n/ FI pdbplus.log FC = 28 FP 3 /stride output for/ FP 2 /failures: 0\n/ FI stride.log FC = 0 FZ = 0 FI naccess.log FC = 6 FP 3 /naccess: using defualt vdw.radii\n/ FP 3 /naccess: using default STD FILE\n/ FI 1cs4.ccf FC = 537 FZ = 51353 FP /^SQ SEQUENCE 52 AA; 5817 MW; 47362A43 CRC32;\n/ FI 1ii7.ccf FC = 462 FZ = 44215 FP /^SQ SEQUENCE 65 AA; 7396 MW; 0CFB92A3 CRC32;\n/ FI 2hhb.ccf FC = 5398 FZ = 533145 FP /^SQ SEQUENCE 141 AA; 15127 MW; 5EC7DB1E CRC32;\n/ // ID scopparse-keep AB domainatrix DL keep AA scopparse IN ../../data/structure/scop.cla.raw IN ../../data/structure/scop.des.raw IN Y IN N IN all.scop FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI all.scop FC = 52 FZ = 809 FP 2 /^ID / // ID domainer-keep AB structure DL keep AA domainer IN ../scopparse-keep/all.scop IN ../pdbplus-keep/ IN IN IN 1 IN domainer_embl.log IN domainer_pdb.log FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^D1CS4A_\n/ FP /^D1II7A_\n/ FI domainer_embl.log FZ = 0 FI domainer_pdb.log FZ = 0 FI d1cs4a_.ent FZ = 29889 FC = 369 FP /^ATOM\s+31\s+CA\s+PHE\s+A\s\d+\s+60.914 -11.143 59.200 1.00 58.07\s+C\s+\n/ FI d1cs4a_.ccf FZ = 40509 FC = 418 FP /SQ SEQUENCE 52 AA; 5817 MW; 47362A43 CRC32;\n/ FI d1ii7a_.ent FZ = 29727 FC = 367 FP /ATOM 1 N ASP A 8 7.977 32.254 19.055 1.00 26.65 N / FI d1ii7a_.ccf FZ = 39748 FC = 413 FP /SQ SEQUENCE 65 AA; 7396 MW; 0CFB92A3 CRC32;/ // ID domainer-keep2 AB structure DL keep AA domainer IN ../../data/structure/all.scop2 IN ../pdbparse-keep2 IN IN IN 1 IN domainer_embl.log IN domainer_pdb.log FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^D1CS4A_\n/ FP /^D1FX2A_\n/ FP /^D4AT1B1\n/ FP /^D4AT1D1\n/ FI domainer_embl.log FZ = 0 FI domainer_pdb.log FZ = 0 FI d1cs4a_.ent FZ = 123201 FC = 1521 FP 1476 /ATOM/ FI d1cs4a_.ccf FZ = 166802 FC = 1684 FP /SQ SEQUENCE 225 AA; 25486 MW; 437C8290 CRC32;\n/ FI d1fx2a_.ent FZ = 152928 FC = 1888 FP 1856 /ATOM/ FI d1fx2a_.ccf FZ = 209167 FC = 2110 FP 235 /RE / FI d4at1b1.ent FZ = 60183 FC = 743 FP 725 /ATOM/ FI d4at1b1.ccf FZ = 82081 FC = 835 FP 93 /RE / FI d4at1d1.ent FZ = 60183 FC = 743 FP 725 /ATOM/ FI d4at1d1.ccf FZ = 82081 FC = 835 FP 93 /RE / // ID contacts-keep AB structure DL keep AA contacts IN ../pdbplus-keep/ IN IN 1 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1ii7\n/ FP /^1cs4\n/ FP /^2hhb\n/ FI 1cs4.con FC = 183 FZ = 3736 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .\n/ FP /NC SM 163; LI .\n/ FP /SM ASP 46 ; CYS 47\n/ FI 1ii7.con FC = 172 FZ = 3545 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 .\n/ FP /NC SM 151; LI .\n/ FP /SM ASP 49 ; LEU 50\n/ FI 2hhb.con FC = 2696 FZ = 58326 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 141; NRES2 .\n/ FP /NC SM 643; LI .\n/ FP /SM VAL 1 ; LEU 2\n/ FI contacts.log FC = 3 FZ = 15 FP /1cs4\n/ FP /1ii7\n/ FP /2hhb\n/ // ID contacts-keep2 AB structure DL keep AA contacts IN ../domainer-keep/ IN IN 1 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^D1II7A_\n/ FP /^D1CS4A_\n/ FI d1cs4a_.con FC = 183 FZ = 3742 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .\n/ FP /NC SM 163; LI .\n/ FP /SM ASP 2 ; ILE 3\n/ FI d1ii7a_.con FC = 172 FZ = 3551 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 .\n/ FP /NC SM 151; LI .\n/ FP /SM ASP 49 ; LEU 50\n/ FI contacts.log FC = 2 FZ = 16 FP /D1II7A_\n/ FP /D1CS4A_\n/ // ID interface-ex AB structure AA interface IN ../pdbplus-keep/2hhb.ccf IN 1 IN 2hhb.con IN FI stdout FC = 1 FP /^2hhb\n/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI 2hhb.con FC = 274 FZ = 7000 FP /CN MO 1; CN1 1; CN2 2; ID1 A; ID2 B; NRES1 141; NRES2 146\n/ FP 152 /^SM / FI interface.log FC = 1 FP /^2hhb\n/ // ID sites-keep AB structure DL keep TI 120 AA sites IN ../pdbplus-keep IN ../domainer-keep IN ../scopparse-keep/all.scop IN 1 IN IN FI stdout FC = 5 FP /^Entries in HetDic 4306\n/ FP /^Entries in Dbase 4306\n/ FP /CCF FILE:.*/1cs4.ccf \([1-3]\/3\)/ FP /CCF FILE:.*/1ii7.ccf \([1-3]\/3\)/ FP /CCF FILE:.*/2hhb.ccf \([1-3]\/3\)/ FI stderr FZ = 315 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI SITES.con FC = 299 FZ = 5173 FP 11 /^ID / FP 3 /^LI ASP 2/ FP /ID PDB 1cs4; DOM d1cs4a_; LIG POP;\n/ FI sites.log FC = 3 FP /^CCF:.*1cs4.ccf HETS:YES NHETS:7 SCOP:YES NDOMS: 1\n/ FP /^CCF:.*1ii7.ccf HETS:YES NHETS:5 SCOP:YES NDOMS: 1\n/ FP /^CCF:.*2hhb.ccf HETS:YES NHETS:5 SCOP:NO NCHN:4\n/ // ID hetparse-ex AB structure AA hetparse IN ../../data/structure/het.txt IN Y IN IN Ehet.dat FP 2 /^Processing/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI Ehet.dat FC = 48 FZ = 949 FP 9 /^NN/ // ID pdbtosp-keep AB structure DL keep AA pdbtosp IN ../../data/structure/pdbtosp.txt IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI Epdbtosp.dat FC = 49 FZ = 422 FP 7 /^EN / FP /^IN XYLA_ACTMI ID; P12851 ACC;\n/ // ######################################################### # # EMBASSY (DOMAINATRIX) # ######################################################### ID cathparse-ex AB domainatrix AA cathparse IN ../../data/structure/caths.list.small IN ../../data/structure/domlist.small IN ../../data/structure/CAT.names.all.small IN IN FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI Ecath.dat FC = 48 FZ = 606 FP 2 /^ID/ FP /CH 0 CHAIN; 156 START; 203 END;\n/ FP /CH 0 CHAIN; 159 START; 202 END;\n/ FP /NR 48\n/ FP /NR 44\n/ FP 2 /SF DNA helicase RuvA subunit, C-terminal domain\n/ FI cathparse.log FC = 8 FZ = 64 FP 4 /^1\.10\.8/ // ID domainseqs-keep AB domainatrix DL keep AA domainseqs IN ../scopparse-keep/all.scop IN ../domainer-keep IN Y IN ../pdbtosp-keep/Epdbtosp.dat IN all_s.scop IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FZ = 38 FP 2 /^\/\/\n/ FI all_s.scop FC = 59 FZ = 1064 FP 2 /^ID / FI domainseqs.log FC = 6 FZ = 78 FP 2 /^NO_ACCESSION_NUMBER\n/ FP 2 /\/\/\n/ FP /^D1CS4A_ +\n/ FP /^D1II7A_ +\n/ // ID domainnr-ex AB domainatrix AA domainnr IN ../domainseqs-keep/all_s.scop IN IN 1 IN 1 IN 5 IN all_nr.scop IN FI stdout FC = 3 FP 1 /^\/\/ / FP 2 /^D1/ FI stderr FC = 15 FP 0 /Error: / FP 0 /Died: / FI all_nr.scop FC = 30 FZ = 527 FP 1 /^ID/ FI domainnr.log FC = 7 FZ = 117 FP 1 /^Retained/ FP 1 /^Rejected/ FP 1 /^\/\/ / // ID domainreso-ex AB domainatrix AA domainreso IN ../domainer-keep/ IN ../scopparse-keep/all.scop IN 2.3 IN all_2.3.scop FI stdout FC = 2 FP 2 /[.]ccf\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI all_2.3.scop FC = 26 FZ = 390 FP 1 /^ID/ FP /SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;\n/ // ID domainsse-keep AB domainatrix DL keep AA domainsse IN ../scopparse-keep/all.scop IN ../domainer-keep IN domainsse.out IN domainsse.log FI stdout FC = 6 FP 2 /^Processing/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI domainsse.out FC = 62 FZ = 1052 FP 2 /^ID / FI domainsse.log FZ = 0 // ID ssematch-ex AB domainatrix AA ssematch IN ../../data/structure/sse.in IN ../domainsse-keep/domainsse.out IN 1 IN res.dcf IN elm.dcf IN FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI res.dcf FC = 33 FZ = 543 FP 1 /^ID / FI elm.dcf FC = 33 FZ = 573 FP 1 /^ID / FP /^SE HH\n/ FI ssematch.log FC = 0 FZ = 0 // ######################################################### # # EMBASSY (DOMALIGN) + seqsearch (DOMSEARCH) # ######################################################### ID domainrep-keep AB domalign DL keep AA domainrep RQ stamp CC requires a modified stamp to be installed IN ../../data/structure/all.scop2 IN 2 IN all_rep1st.scop FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 12 FZ = 1008 FP 6 /stamp/ FI all_rep1st.scop FC = 104 FZ = 1785 FP 4 /^ID/ // ID domainalign-keep AB domalign DL keep AA domainalign PP mkdir daf RQ stamp CC requires a modified stamp to be installed IN ../../data/structure/all.scop2 IN ../domainer-keep2 IN 4 IN 1 IN N IN daf IN IN FI stderr FC = 15 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 108 FP 4 /^stamp/ FI 54894.ent FC = 1461 FZ = 117967 FP 11 /^REMARK/ DI daf DF 54894.daf DF 55074.daf ## FI daf/54894.daf ## FC = 21 ## FZ = 856 ## FP 6 /^# XX/ FI 55074.ent FC = 3343 FZ = 270409 FP 11 /^REMARK/ ## FI daf/55074.daf ## FC = 36 ## FZ = 1773 ## FP 6 /^# XX/ FI domainalign.log FC = 14 FZ = 574 FP 14 /^Replaced/ // ID allversusall-ex AB domalign AA allversusall IN ../../data/structure/allversusall/ IN IN FI stdout FC = 2 FP /swtiny1.fasta$/ FP /swtiny2.fasta$/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI swtiny1.out FC = 10 FZ = 280 FP /1 Q9WVI4 : 2 Q9ERL9 : 90.48\n/ FP /2 Q9ERL9 : 3 Q9DGG6 : 58.28\n/ FP /3 Q9DGG6 : 4 Q99396 : 52.26\n/ FP /4 Q99396 : 5 Q99280 : 83.41\n/ FI swtiny2.out FC = 3 FZ = 84 FP /1 O58452 : 2 O30129 : 82.42\n/ FP /1 O58452 : 3 O26938 : 75.56\n/ FP /2 O30129 : 3 O26938 : 71.43\n/ FI allversusall.log FC = 4 FP 2 /^\/\/\n/ FP /swtiny1.fasta$/ FP /swtiny2.fasta$/ // ######################################################### # # EMBASSY (DOMSEARCH) + seqalign (DOMALIGN) # ######################################################### ID seqsearch-keep RQ blastpgp ## Uses blastpgp to search ## blastpgp generates 4 warning messages ## (WARNING so the test pattern misses it) in stderr AB domsearch DL keep AA seqsearch IN 2 IN ../domainalign-keep/daf IN ../../data/structure/swsmall IN IN 0.0001 IN 100 IN IN IN 2 FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 6 FP 2 /^blastpgp/ FI 54894.dhf FC = 80 FZ = 13751 FP 40 /^>/ FI 55074.dhf FC = 200 FZ = 37365 FP 100 /^>/ FI seqsearch.log FC = 4 FP 2 /[.]daf\n/ FP 2 /^\/\/\n/ // ID seqfraggle-keep AB domsearch DL keep AA seqfraggle IN ../seqsearch-keep IN 50 IN FI stdout FC = 2 FP /Processing .*54894.dhf\n/ FP /Processing .*55074.dhf\n/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI 54894.dhf FZ = 13471 FC = 80 FP 40 /^>/ FI 55074.dhf FZ = 35123 FC = 188 FP 94 /^>/ // ID seqnr-keep AB domsearch DL keep AA seqnr PP mkdir hitsnr PP mkdir hitsred IN ../seqfraggle-keep IN N IN Y IN ../domainalign-keep/daf IN 1 IN 70 IN hitsnr IN Y IN hitsred IN FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP 2 /^Processing/ FI seqnr.log FC = 4 FP 2 /^\/\/\n/ FP 2 /[.]dhf\n/ DI hitsnr DF 54894.dhf DF 55074.dhf ## FI hitsnr/54894.dhf ## FZ = 1351 ## FC = 8 ## FP 4 /^>/ ## hitsnr/55074.dhf ## FZ = 2512 ## FC = 14 ## FP 7 /^>/ DI hitsred DF 54894.dhf DF 55074.dhf ## FI hitsred/54894.dhf ## FZ = 12120 ## FC = 72 ## FP 36 /^>/ ## FI hitsred/55074.dhf ## FZ = 32611 ## FC = 174 ## FP 87 /^>/ // ID seqsort-keep AB domsearch DL keep AA seqsort IN ../seqnr-keep/hitsnr IN 10 IN Y IN Y IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI fam.dhf FC = 22 FZ = 3863 FP 11 /^> / FI oth.dhf FC = 0 FZ = 0 FI 54894.dhf FC = 8 FZ = 1351 FP 4 /^> / FI 55074.dhf FC = 14 FZ = 2512 FP 7 /^> / // ID seqwords-ex AB domsearch AA seqwords IN ../../data/structure/seqwords.terms IN ../../data/structure/seqwords.seq IN seqwords.dhf FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI seqwords.dhf FC = 2 FZ = 531 FP /^> Q60150\^.\^1\^312\^SCOP\^.\^0\^Alpha and beta proteins/ // ID seqalign-keep AB domalign AA seqalign DL keep TI 300 RQ clustalw ## Apparently requires clustalw 1.83 for long filenames ## clustalw 1.82 failed with 'unable to read .aln file' ## this was a clustalw error message ## renaming the files and running clustalw worked IN 2 IN ../domainalign-keep/daf IN ../seqsearch-keep IN 1 IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 6344 FP 144 /Sequence \d+: .* \d+ aa\n/ FI 54894.daf FC = 98 FZ = 6987 FP 2 /d4at1b1_0/ FP 2 /d4at1d1_1/ FI 55074.daf FC = 527 FZ = 42660 FP 5 /d1cs4a__0/ FP 5 /d1fx2a__1/ FI seqalign.log FC = 4 FP 2 /[.]daf\n/ FP 2 /^\/\/\n/ // ######################################################### # # EMBASSY (SIGNATURE) # ######################################################### ID siggen-keep AB signature DL keep AA siggen IN ../domainalign-keep/daf IN 2 IN 5 IN 1 IN EBLOSUM62 IN 15 IN 0 IN Y IN FI stderr FC = 16 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 54894.sig FC = 136 FZ = 1367 FP 15 /^IN / FI 55074.sig FC = 330 FZ = 3140 FP 38 /^IN / // ID siggenlig-keep AB signature DL keep AA siggenlig IN ../sites-keep/SITES.con IN ../pdbplus-keep IN ../domainer-keep IN 1 IN 1 IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FZ = 0 FI 101.1.F.#.1cs4.d1cs4a_.sig FC = 62 FZ = 610 FP /^IN / FI 101.2.F.#.1ii7.d1ii7a_.sig FC = 30 FZ = 318 FP /^IN / FI FOK.1.F.#.1cs4.d1cs4a_.sig FC = 22 FZ = 219 FP /^IN / FI HEM.1.F.#.2hhb...sig FC = 150 FZ = 1415 FP /^IN / FI HEM.2.F.#.2hhb...sig FC = 150 FZ = 1415 FP /^IN / FI HEM.3.F.#.2hhb...sig FC = 166 FZ = 1563 FP /^IN / FI HEM.4.F.#.2hhb...sig FC = 134 FZ = 1267 FP /^IN / FI MG.1.F.#.1cs4.d1cs4a_.sig FC = 46 FZ = 441 FP /^IN / FI MN.1.F.#.1ii7.d1ii7a_.sig FC = 38 FZ = 373 FP /^IN / FI PO4.1.F.#.2hhb...sig FC = 30 FZ = 290 FP /^IN / FI POP.1.F.#.1cs4.d1cs4a_.sig FC = 62 FZ = 590 FP /^IN / FI siggenlig.log FC = 0 FZ = 0 // ID libgen-ex AB signature AA libgen RQ hmmer RQ sam-t2k IN ../domainalign-keep/daf IN EBLOSUM62 IN 2 IN FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 54894.disc FC = 107 FZ = 14810 FP /Length\s+94\n/ FI 55074.disc FC = 265 FZ = 38174 FP /Length\s+252\n/ // ID matgen3d-ex AB signature AA matgen3d IN 1 IN ../scopparse-keep/all.scop IN ../domainer-keep IN 1 IN IN IN FI stderr FC = 22 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI stdout FC = 0 FZ = 0 FI matgen3d.calc FC = 128 FZ = 3801 FP /SUMiNijArr/ FI matgen3d.log FC = 182 FZ = 2686 FP 1 /D1CS4A/ FP 1 /D1II7A_/ FI matgen3d.out FC = 28 FZ = 3563 FP 1 /AU -0.01 1.19 0.91 0.50 1.19 0.68 -0.11 2.00 1.19 0.35 -0.11 0.91 2.29 0.35 2.29 1.60 1.19 -2.20 2.29 1.19 -2.20 -2.20 -2.20 -2.64/ // ID sigscan-ex AB signature AA sigscan IN ../siggen-keep/54894.sig IN ../../data/structure/swsmall IN IN IN IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 5 / ok\n/ FI SIGSCAN.dhf FC = 200 FP /> P00478/ FI SIGSCAN.aln FC = 1113 FZ = 73700 FP /^SIGNATURE - ----------\*-\*--------------------------\*-------------\n/ // ID sigscanlig-ex AB signature AA sigscanlig PP mkdir lhf PP mkdir aln PP mkdir results IN ../siggenlig-keep IN ../../data/structure/swtiny IN IN 1 IN IN IN IN lhf IN aln IN results FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 DI lhf DF Q99396^.^262^473^.lhf DF Q9DGG6^.^380^560^.lhf DF Q9ERL9^.^480^631^.lhf DF Q9WVI4^.^516^664^.lhf DI aln DF Q99396^.^262^473^.aln DF Q9DGG6^.^380^560^.aln DF Q9ERL9^.^480^631^.aln DF Q9WVI4^.^516^664^.aln DI results DF Q99396^.^262^473^.results DF Q9DGG6^.^380^560^.results DF Q9ERL9^.^480^631^.results DF Q9WVI4^.^516^664^.results // ID rocon-ex AB signature AA rocon IN ../../data/structure/rocon/rocon.dhf IN ../../data/structure/rocon.valid IN 10 IN 1 IN rocon.hits FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rocon.hits FC = 9 FZ = 308 FP 3 /^TRUE / FP 2 /^FALSE / FP 2 /^CROSS / FP 1 /^UNKNOWN / // ID rocplot-ex AB signature AA rocplot IN ../../data/structure/rocplot/hitsin IN 2 IN 2 IN 1 IN IN IN IN IN FI stderr FC = 11 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^Processing / FI _rocplot FC = 12 FZ = 353 FP /^plot "_rocplot_dat0" smooth bezier title "Combined dataset \(0.185\)"\n/ FI _rocplot_dat0 FC = 81 FZ = 1242 FP /^0.625 0.214\n/ FI _classplot FC = 9 FZ = 580 FP /^plot "_classplot_dat0" .* "_classplot_dat4" .* title "False hits"\n/ FI _classplot_dat0 FC = 81 FZ = 1315 FP /^80.000 0.375\n/ FI _classplot_dat1 FC = 81 FZ = 1316 FP /^80.000 0.100\n/ FI _classplot_dat2 FC = 81 FZ = 1320 FP /^80.000 0.050\n/ FI _classplot_dat3 FC = 81 FZ = 1318 FP /^80.000 0.100\n/ FI _classplot_dat4 FC = 81 FZ = 1316 FP /^80.000 0.375\n/ FI _summary FC = 11 FZ = 333 FP /ROC50 == 0.185 \(combined\)/ FI rocplot.log FC = 33 FP /^rocn\[0\]:/ FP /^numfiles: 2\n/ // ###################################### # EMNU ####################################### ID emnu-ex AB emnu AA emnu CL -explode IK  IK IK y FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FK stdout FC > 3 FP /^emnu version: 1.0.5\n/ FP /^EMBOSS Simple Menu\n/ FP /ALPHABETIC LISTING OF ALL PROGRAMS/ FP /ALIGNMENT GLOBAL/ // ####################################### # ESIM4 ####################################### ID esim4-ex AB esim4 AA esim4 ## Test example copied from est2genome ## Similar results - possible longer alignment at 3' end of EST. IN tembl:hs989235 IN tembl:hsnfg9 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hs989235.esim4 FC = 7 FP /^seq1 = HS989235, 495 bp\n/ FP /^seq2 = HSNFG9 \(HSNFG9\), 33760 bp\n/ FP /^1-193 \(25686-25874\) 92% <-\n/ FP /^194-407 \(26279-26492\) 98% <-\n/ FP /^408-487 \(27391-27469\) 88%\n/ // ####################################### # HMMER # demo directory ../../data/hmm # has example files from the hmmer 2.1.1 tutorial ####################################### ID ehmmbuild-ex-keep AB hmmer AA ehmmbuild DL keep CL ../../data/hmm/globins50.msf globin.hmm -auto FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 32 FP /^Maximum score: 248.11 bits\n/ FI globin.hmm FC = 456 FP /^HMMER2.0\n/ FP /^CKSUM 5854\n/ FI globins50.out2 FC = 260 FP /^#=SQ HBB2_TRICR 0.5133 - - 0..0::0 -\n/ FI globins50.out3 FC = 436 FP /^M 0.00 0.00 0.00 0.00 0.00 3.32 0.00 .* 1.17 0.00 7.14 0.00 0.00 \n/ // ID ehmmcalibrate-ex-keep AB hmmer AA ehmmcalibrate TI 120 DL keep ## copy the input file because it will be updated ## Provide a seed value to get reproducible output for validation PP cp ../ehmmbuild-ex-keep/globin.hmm ./ CL globin.hmm -seed 1079460101 -auto FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globin.ehmmcalibrate FC = 13 FP /Number of samples: 5000\n/ FI globin.out2 FC = 35 FP /% Statistical details of theoretical EVD fit:\n/ FI globin.hmm FC = 458 FP /^COM ehmmbuild ../../data/hmm/globins50.msf globin.hmm -auto\n/ FP /^COM ehmmcalibrate globin.hmm -seed 1079460101 -auto\n/ FP 2 /^COM/ // ID ehmmsearch-ex AB hmmer AA ehmmsearch CL ../../data/hmm/Artemia.fa ../ehmmcalibrate-ex-keep/globin.hmm -auto FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 26 FP / Total hits: 1\n/ FI s13421.ehmmsearch FC = 24 FP /S13421 1/1 303 347 .. 1 45 \[. 12.7 0.089\n/ // ID ehmm-own-keep1 AB hmmer AA ehmmbuild DL keep CL ../../data/hmm/rrm.slx rrm.hmm FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 70\n/ FI rrm.hmm FC = 236 FP /^LENG 72\n/ FI rrm.out2 FC = 216 FP /^#=SQ CABA_MOUSE\/77-148 0.8349 CABA_MOUSE\/77-148 - 0..0::0 -\n/ FI rrm.out3 FC = 214 FP /^M 2.09 0.84 [0. ]+ 20.78 0.00 30.46 0.83 [0. ]+ 13.00 [0. ]+ \n/ // ID ehmm-own-keep2 AB hmmer AA ehmmbuild CL ../../data/hmm/fn3.slx fn3.hmm QQ cp fn3.hmm ../ehmm-own-keep1/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 109\n/ FI fn3.hmm FC = 272 FP /^LENG 84\n/ FI fn3.out2 FC = 444 FP /^#=SQ 7LES_DROVI/1917-1997 1.1291 7LES_DROVI/1917-1997 - 0..0::0 -\n/ FI fn3.out3 FC = 250 FP /^M 4.96 0.00 18.09 4.46 0.00 9.88 0.00 0.00 .* 0.00 1.13 \n/ // ID ehmm-own-keep3 AB hmmer AA ehmmbuild CL ../../data/hmm/pkinase.slx pkinase.hmm QQ cp pkinase.hmm ../ehmm-own-keep1/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 67\n/ FI pkinase.hmm FC = 824 FP /^LENG 268\n/ FI pkinase.out2 FC = 552 FP /^#=SQ ABL1_CAEEL/296-547 0.9915 ABL1_CAEEL/296-547 - 0..0::0 -\n/ FI pkinase.out3 FC = 802 FP /^M 0.00 1.06 2.00 3.06 5.97 .* 3.91 1.03 4.04 8.98 0.00 0.97 \n/ // ID ehmm-own-keep AB hmmer PP cat ../ehmm-own-keep1/*.hmm > myhmms AA ehmmcalibrate DL keep TI 300 CL myhmms -seed 1079460101 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI myhmms FC = 1338 FP /^LENG 268\n/ FI myhmms.ehmmcalibrate FC = 23 FP /^\n/ FI myhmms.out2 FC = 110 FP /^HMM: 7LES_DROME/2209-2481\n/ FP /^chi-sq statistic = 45.1950\n/ // ID ehmm-own2-keep1 AB hmmer AA ehmmbuild DL keep CL ../../data/hmm/rrm.sto -sf stockholm myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 70\n/ FI myhmms FC = 236 FP /^LENG 72\n/ FI rrm.out2 FC = 216 FP /^#=SQ CABA_MOUSE\/77-148 0.8349 CABA_MOUSE\/77-148 - 0..0::0 -\n/ FI rrm.out3 FC = 214 FP /^M 2.09 0.84 [0. ]+ 20.78 0.00 30.46 0.83 [0. ]+ 13.00 [0. ]+ \n/ // ID ehmm-own2-keep2 AB hmmer AA ehmmbuild CL -append ../../data/hmm/fn3.slx ../ehmm-own2-keep1/myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 109\n/ FI fn3.out2 FC = 444 FP /^#=SQ 7LES_DROVI/1917-1997 1.1291 7LES_DROVI/1917-1997 - 0..0::0 -\n/ FI fn3.out3 FC = 250 FP /^M 4.96 0.00 18.09 4.46 0.00 9.88 0.00 0.00 .* 0.00 1.13 \n/ // ID ehmm-own2-keep3 AB hmmer AA ehmmbuild CL -append ../../data/hmm/pkinase.slx ../ehmm-own2-keep1/myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 67\n/ FI pkinase.out2 FC = 552 FP /^#=SQ ABL1_CAEEL/296-547 0.9915 ABL1_CAEEL/296-547 - 0..0::0 -\n/ FI pkinase.out3 FC = 802 FP /^M 0.00 1.06 2.00 3.06 5.97 .* 3.91 1.03 4.04 8.98 0.00 0.97 \n/ // ID ehmm-own2-keep AB hmmer AA ehmmcalibrate DL keep TI 300 PP cp ../ehmm-own2-keep1/myhmms . CL myhmms -seed 1079460101 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI myhmms FC = 826 FP /^LENG 268\n/ FI myhmms.ehmmcalibrate FC = 13 FP /^\n/ FI myhmms.out2 FC = 34 FP /^HMM: 7LES_DROME/2209-2481\n/ FP /^chi-sq statistic = 48.8891\n/ // ID ehmmpfam-ex AB hmmer AA ehmmpfam CL ../../data/hmm/7LES_DROME ../ehmm-own-keep/myhmms IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 48 FP /^\n/ FP /^ CS QDRREWEAHERRLETAGTHRLTGIKPGSGYSLWVQAH \n/ FP /^ RF QDRREWEAHERRLETAGTHRLTGIKPGSGYSLWVQAH \n/ FP /^ ttpstsnttttllllllltytvyvvvvvsasssggsg<-\*\n/ FP /^ +\+\+\+\+ \+ \+\+\+\+l \+ \+\+ \+ \+ \+\+\+s \+ \+ \n/ FP /^ 7LES_DROME 1846 QDRREWEAHERRLETAGTHRLTGIKPGSGYSLWVQAH 1882 \n/ FI 7les_drome.ehmmpfam FC = 18 FP /^7LES_DROME\/1799-1891: domain 1 of 1, from 1799 to 1882: score 32.1, E = 2.5e-06\n/ FP /^7LES_DROME\/2209-2481 1\/1 2209 2476 .. 1 268 \[\] 115.9 7.6e-31\n/ // ID ehmmalign-keep AB hmmer AA ehmmalign DL keep CL ../ehmmbuild-ex-keep/globin.hmm ../../data/hmm/globins630.fa globins630.ali FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Alignment saved in file globins630.ali\n/ FI globins630.ali FC = 6952 FP /^#=SQ HBB_HUMAN 1.0000 - - 0..0::0 -\n/ FP 5 /^HBB_HUMAN [.]+\n/ FP /^HBB_HUMAN L.DN...L.KG....TFAT.LS.EL...H.CDKLHVDPE.NFRLL.GNVL\n/ // ID ehmmconvert-ex AB hmmer AA ehmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm.hmm\n/ FI rrm.hmm FC = 237 FP /^LENG 72\n/ // ID ehmmconvert-exb AB hmmer AA ehmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm -format b FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm.hmm\n/ FI rrm.hmm FC = 23 FP 4 /rrm/ // ID ehmmconvert-exg AB hmmer AA ehmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm -format g FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm.hmm\n/ FI rrm.hmm FC = 91 FP /^!!AA_PROFILE 1.0\n/ FP /^\(Peptide\) HMMCONVERT v2.1.1 Length: 72 rrm\|\|\n/ FP /^ F -364 -346 -598 -534 .* -260 110 111\n/ // ID ehmmconvert-exx AB hmmer AA ehmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm -format x FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm.hmm\n/ FI rrm.hmm FP /^!!AA_PROFILE 1.0\n/ FP /^\(Peptide\) HMMCONVERT v2.1.1 Length: 72 rrm\|\|\n/ FP /^ F -364 -346 -598 -534 .* -260 110 111 116 137\n/ // ID ehmmemit-ex AB hmmer AA ehmmemit CL ../../data/hmm/rrm.hmm -seed 1079460101 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rrm.ehmmemit FC = 30 FP 10 /^>seq[0-9]+ +\n/ FP /^VYITNLPPGVQKQELFDVKDTYFGEHGPVVRFNISRDDDDTQTGEASGFG\n/ FP /^EDAEAALENLRGIKINNRKLHI\n/ // ID ehmmindex-keep AB hmmer AA ehmmindex DL keep PP cp ../ehmm-own-keep/myhmms myhmms CL myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI myhmms FC = 1338 FP /^LENG 268\n/ FI myhmms.gsi FZ = 304 FP /7LES_DROME/ // ID ehmmfetch-ex AB hmmer AA ehmmfetch CL ../ehmmindex-keep/myhmms 7LES_DROME/1799-1891 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.ehmmfetch FC = 274 FP /^NAME 7LES_DROME/1799-1891\n/ // ID ealistat-ex AB hmmer AA ealistat CL ../ehmmalign-keep/globins630.ali IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins630.ealistat FC = 14 FP /^Number of sequences: 630\n/ FP /^Average length: 145.1\n/ FP /^Alignment length: 469\n/ FP /^Average identity: 25%\n/ FP /^Most distant seq: 6%\n/ // ####################################### # MEME ####################################### ID meme-ex AB meme AA meme CL -protein IN ../../data/memepep.dat IN IN 3 IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI carp_rhich.meme FC = 359 FP /^MOTIF\s+1\s+width =\s+8\s+sites =\s+5.0\n/ FP /MOTIF\s+2\s+width =\s+15\s+sites =\s+5.0\n/ FP /^MOTIF\s+3\s+width =\s+16\s+sites =\s+5.0\n/ FP 3 /^MOTIF/ // ####################################### # MSE ####################################### ID mse-ex AB mse AA mse CL ../../data/dna.msf msf::mse.msf IK :21 IK :1 up IK acgt:25 28 delete IK ----:exit FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FK stdout FZ = 2876 FP /exit/ FI mse.msf FC = 25 FP /^MSFM2 ACGTACGTACGTACGTACGTacgt....ACGTACGTACGTACGTACGTAC\n/ FP 9 /^MSFM/ // ####################################### # MYEMBOSS ####################################### ID myseq-ex AB myemboss AA myseq IN tembl:paamir IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir.myseq FC = 5 FP /^Usa: tembl-id:PAAMIR\n/ FP /^Length: 2167\n/ // ####################################### # PHYLIP 3.5 ####################################### ID eclique-ex AB phylip AA eclique IN ../../data/evolution/clique.dat IN IN IN IN IN FI eclique.outfile FC = 31 FP /^Characters: \( 1 2 3 6\)\n/ FP /^ 2 1 3 6\n/ FI eclique.treefile FC = 1 FP /^\(\(\(Delta,Epsilon\),Gamma\),Alpha,Beta\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID econsense-ex AB phylip AA econsense IN ../../data/evolution/consense.dat IN IN IN FI econsense.outfile FC = 74 FP s /^ F\n I\n C\n/ FP /^\.\.\*\.\*\.\.\.\.\.\s+4\.00\n/ FI consense.treefile FC = 2 FP /^\(A:9.0,\(\(E:9.0,\(\(\(I:9.0,F:9.0\):9.0,\(\(D:9.0,\(J:9.0,H:9.0\):4.0\)/ FP /\(J:9.0,H:9.0\):4.0\):6.0,C:9.0\):6.0\):2.0,G:9.0\):6.0\):9.0,\n/ FP /^B:9.0\):9.0\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^\n/ // ID econtml-ex AB phylip AA econtml IN ../../data/evolution/contml.dat IN IN IN IN IN IN IN IN IN FI econtml.outfile FC = 31 FP /^Ln Likelihood = 33\.29060\n/ FP /^ 3 Chinese 0.00221 \( -0.02034, 0.03710\)\n/ FI econtml.treefile FC = 2 FP /^\(African:0.08464,\(American:0.02094,\(Australian:0.05959,Chinese:0.00221\)/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID econtrast-ex AB phylip AA econtrast IN ../../data/evolution/contrast.dat IN ../../data/evolution/contrast.tree IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI econtrast.outfile FC = 27 FP /^ 3.9423 1.7028\n/ FP /^ 1.0000 0.4319\n/ FP /^ 1.0000 0.6566\n/ // ID ednacomp-ex AB phylip AA ednacomp CL -stepoutput IN ../../data/evolution/dnacomp.dat IN IN IN IN IN FI ednacomp.outfile FC = 36 FP /total number of compatible sites is 11.0\n/ FP / 0[!] 2 1 3 2 0 2 1 1 1\n/ FP / 0 [!] YYNYYYYYY\n/ FP /One most parsimonious tree found:\n/ FI ednacomp.treefile FC = 1 FP /\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ednadist-ex AB phylip AA ednadist IN ../../data/evolution/dnadist.dat IN IN IN IN FI ednadist.outfile FC = 6 FP / 5\n/ FP /^Alpha 0.0000 0.2997 0.7820 1.1716 1.4617\n/ FI stderr FC = 10 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ednainvar-ex AB phylip AA ednainvar IN ../../data/evolution/dnainvar.dat IN FI ednainvar.outfile FC = 109 FP /^ AAAG 2\n/ FP /^ 1113 3\n/ FP /^ III: \(\(Alpha.*,Delta.*\),\(Beta.*,Gamma.*\)\)\n/ FP /^ III 0 - 0 = 0 1.0000 no\n/ FP /^ Quadratic invariant = 4.0\n/ FP 3 /^ Quadratic invariant =/ FP / Tree III: 5.0\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## stdout has one blank line FI stdout FC = 1 FP /^\n/ // ID ednaml-ex AB phylip AA ednaml ## may need to play with the input file format for this one CL -categories -catnum 2 -catvals "1.0 3.2" -catprob "0.4 0.6" CL -lambda 1.5 -autog -printdata -progress IN ../../data/evolution/dnaml.dat IN IN IN IN IN IN IN IN FI ednaml.outfile FC = 67 FP /^ G 0.24615\n/ FP /^ 2 3.200 0.600\n/ FP /^Ln Likelihood = -71.831[0-9][0-9]\n/ FP /^ 2 +Beta +0.00003 +\( +zero, +0.41145\)\n/ FP /^ 1 +Gamma +1.35995 +\( +zero, +3.26620\) \*\*\n/ FP /^ 2122121111 212\n/ FI ednaml.treefile FC = 2 FP /^\(\(\(Epsilon:0.00012,Delta:0.30872\):3.33144,Beta:0.00012\):0.08840,\n/ FP /^Gamma:1.35995,Alpha:0.24900\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 8 /^./ // ID ednamlk-ex AB phylip AA ednamlk CL -categories -catnum 2 -catvals "1.0 3.2" -catprob "0.4 0.6" CL -lambda 1.5 IN ../../data/evolution/dnaml.dat IN IN IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ednamlk.outfile FC = 57 FP /Transition/transversion parameter = 1.5230/ FP /^ \!\s+\+-------------Gamma \n/ FP /^Ln Likelihood = -72.40499\n/ FP /^ 3 4 3.40036 3.40036\n/ FI ednamlk.treefile FC = 2 FP /^\(\(Delta:0.15834,Epsilon:0.15834\):3.40036,\(Gamma:0.80621,\n/ FP /^\(Alpha:0.17218,Beta:0.17218\):0.63403\):2.75249\);\n/ // ID ednapars-ex AB phylip AA ednapars IN ../../data/evolution/dnapars.dat IN IN IN IN FI ednapars.outfile FC = 21 FP /^requires a total of 19.000\n/ FP /^ \+--Epsilon.*\n/ FI ednapars.treefile FC = 1 FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ednapenny-ex AB phylip AA ednapenny IN ../../data/evolution/dnapenny.dat IN IN IN IN FI ednapenny.outfile FC = 207 FP /^ 9 trees in all found\n/ FP /^ \! \+-----6 \+-----Gamma2 \n/ FI ednapenny.treefile FC = 9 FP /^\(Alpha1,\(\(\(\(\(Delta,Epsilon\),Gamma2\),Gamma1\),\(Beta2,Beta1\)\),Alpha2\)\)\[0.1111\];\n/ FP 3 /\(Gamma2,Gamma1\)/ FP 9 /\(Delta,Epsilon\),/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID edollop-ex AB phylip AA edollop IN ../../data/evolution/dollop.dat IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edollop.outfile FC = 28 FP /^One most parsimonious tree found:\n/ FP 1 /^requires a total of 3.000\n/ FI edollop.treefile FC = 1 FP /^\(Delta,\(Epsilon,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ // ID edolpenny-ex AB phylip AA edolpenny IN ../../data/evolution/dolpenny.dat IN IN IN IN FI edolpenny.outfile FC = 67 FP /^ 3 trees in all found\n/ FP 1 /^ \+--6 \+--5 \n/ FI edolpenny.treefile FC = 3 FP /^\(Delta,\(Epsilon,\(Gamma1,\(Alpha2,\(\(Beta2,Beta1\),Alpha1\)\)\)\)\)\[0.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(Beta2,Beta1\),\(Alpha2,Alpha1\)\)\)\)\)\[0.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(\(Beta2,Beta1\),Alpha2\),Alpha1\)\)\)\)\[0.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID efactor-ex AB phylip AA efactor IN ../../data/evolution/factor.dat IN FI efactor.outfile FC = 5 FP /^ +4 +8\n/ FP /^Alpha 11100000\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP 1 /^./ // ID efitch-ex AB phylip AA efitch IN ../../data/evolution/fitch.dat IN IN IN IN FI efitch.outfile FC = 47 FP /^ 7 Populations\n/ FP /^Sum of squares = 0.01417\n/ FP /^ 1 Mouse 0.77028\n/ FP /^ 1 2 0.41923\n/ FP /^ 2 Gibbon 0.35442\n/ FI fitch.treefile FC = 2 FP /^\(Mouse:0.77028,\(\(\(\(Human:0.11417,Chimp:0.15503\):0.03705,\n/ FP /^Gorilla:0.15677\):0.01693,Orang:0.29628\):0.05289,Gibbon:0.35442\):0.41923,Bovine:0.91632\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID egendist-ex AB phylip AA egendist IN ../../data/evolution/gendist.dat IN IN FI egendist.outfile FC = 6 FP /^ 5\n/ FP /^Chinese 0.0807 0.2347 0.0000 0.0539 0.0633\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ekitsch-ex AB phylip AA ekitsch IN ../../data/evolution/kitsch.dat IN IN FI ekitsch.outfile FC = 48 FP /^ 7 Populations\n/ FP /^Sum of squares = 0.168\n/ FP /^ 6 Human 0.13460 0.81151\n/ FP /^ 5 6 0.02776 0.67691\n/ FP /^ 6 Chimp 0.13460 0.81151\n/ FI ekitsch.treefile FC = 3 FP /^\(\(\(\(\(\(Human:0.13460,Chimp:0.13460\):0.02776,Gorilla:0.16236\):0.07664,\n/ FP /^Orang:0.23900\):0.06461,Gibbon:0.30360\):0.43105,Mouse:0.73465\):0.07686,\n/ FP /^Bovine:0.81151\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID emix-ex AB phylip AA emix IN ../../data/evolution/mix.dat IN IN IN IN IN FI emix.outfile FC = 84 FP 4 /^requires a total of 9.000\n/ FP /^ 4 trees in all found\n/ FP 2 /^--1 \! \+--Delta +\n/ FI emix.treefile FC = 4 FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0.2500\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.2500\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0.2500\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0.2500\];\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eneighbor-ex AB phylip AA eneighbor IN ../../data/evolution/neighbor.dat IN IN IN IN IN FI eneighbor.outfile FC = 40 FP /^ 7 Populations\n/ FP /^ \+--2 \+----------------------Mouse \n/ FP /^ 1 Mouse 0.76891\n/ FP /^ 2 1 0.42027\n/ FP /^ 2 Gibbon 0.35793\n/ FI eneighbor.treefile FC = 2 FP /^\(Orang:0.28469,\(Gorilla:0.15393,\(Chimp:0.15167,Human:0.11753\):0.03982\):0.02696,\(\(Bovine:0.91769,\n/ FP /^Mouse:0.76891\):0.42027,Gibbon:0.35793\):0.04648\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID epenny-ex AB phylip AA epenny IN ../../data/evolution/penny.dat IN IN IN IN FI epenny.outfile FC = 66 FP /^ 3 trees in all found\n/ FP 3 /^ remember: this is an unrooted tree\!\n/ FP /^ \! \+-----Alpha2 \n/ FI epenny.treefile FC = 3 FP /^\(Alpha1,\(\(Alpha2,\(\(Epsilon,Delta\),Gamma1\)\),\(Beta2,Beta1\)\)\)\[0.3333\];\n/ FP /^\(Alpha1,\(Alpha2,\(\(\(Epsilon,Delta\),Gamma1\),\(Beta2,Beta1\)\)\)\)\[0.3333\];\n/ FP /^\(Alpha1,\(\(Alpha2,\(Beta2,Beta1\)\),\(\(Epsilon,Delta\),Gamma1\)\)\)\[0.3333\];\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^\n/ // ID eprotdist-ex AB phylip AA eprotdist IN ../../data/evolution/protdist.dat IN IN FI eprotdist.outfile FC = 6 FP /^Gamma 0.88304 0.45192 0.00000 1.30693 1.21582\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eprotpars-ex AB phylip AA eprotpars IN ../../data/evolution/protpars.dat IN IN IN IN FI eprotpars.outfile FC = 58 FP /^ 3 trees in all found\n/ FP 1 /^ \! \+--Beta \n/ FP 2 /^ \! +\+-+Beta +\n/ FI eprotpars.treefile FC = 3 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID erestml-ex AB phylip AA erestml IN ../../data/evolution/restml.dat IN IN IN IN FI erestml.outfile FC = 42 FP /^Ln Likelihood = -40.35857\n/ FP /^ 1 Gamma 0.11430 \( 0.11177, 0.11683\) \*\*\n/ FI erestml.treefile FC = 2 FP /^\(\(Epsilon:0.00005,Delta:0.01458\):0.05855,\(Gamma:0.11430,\n/ FP /^Beta:0.00008\):0.00002,Alpha:0.02468\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eseqboot-ex AB phylip AA eseqboot IN ../../data/evolution/seqboot.dat IN IN IN IN IN FI eseqboot.outfile FC = 600 FP 11 /^Alpha AAAAAA\n/ FP 17 /^Beta AAACCC\n/ FP 25 /^\S+ +AAACCC\n/ FP 100 /^Alpha/ FI stderr FC = 11 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ####################################### # PHYLIP 3.6 ####################################### ID fclique-ex AB phylipnew AA fclique IN ../../data/evolution/clique.dat IN FI clique.fclique FC = 31 FP /^Characters: \( 1 2 3 6\)\n/ FP /^ 2 1 3 6\n/ FI clique.treefile FC = 1 FP /^\(\(\(Delta,Epsilon\),Gamma\),Alpha,Beta\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 7 FP 3 /^./ // ID fclique-all AB phylipnew AA fclique CL -ancfile ../../data/evolution/clique.ancestral CL -factorfile ../../data/evolution/clique.factors CL -weights ../../data/evolution/clique.weights IN ../../data/evolution/clique.dat IN FI clique.fclique FC = 58 FP /^ 11223 4\n/ FP /^Actual Characters: \( 1 4\)\n/ FP /^Binary Characters: \( 1 2 6\)\n/ FP 2 /Tree and binary characters:/ FI clique.treefile FC = 2 FP /^\(\(\(Alpha,Beta\),Gamma\),Delta,Epsilon\)\[0.5000\];\n/ FP /^\(\(Alpha,Gamma,Epsilon\),Delta,Beta\)\[0.5000\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 7 FP 3 /^./ // ID fconsense-ex AB phylipnew AA fconsense IN ../../data/evolution/consense.dat IN FI consense.fconsense FC = 77 FP /^ 10. C\n/ FP /^\.\.\*\.\*\.\.\.\.\.\s+4\.00\n/ FI consense.treefile FC = 2 FP /^B:9.0\):9.0,A:9.0\);\n/ FP /\(\(H:9.0,J:9.0\):4.0,D:9.0\)/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 7 FP 3 /^./ // ID fcontml-ex AB phylipnew AA fcontml CL -printdata IN ../../data/evolution/contml.dat IN IN FI contml.fcontml FC = 67 FP /^Ln Likelihood = 20.7312[0-9]\n/ FP /^ 3 Chinese 0.00301 \( -0.03824, 0.06681\)\n/ FI contml.treefile FC = 2 FP /\(American:0.00000,\(Australian:0.13759,Chinese:0.00301\):0.09982\)/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 10 /^./ // ID fcontrast-ex AB phylipnew AA fcontrast IN ../../data/evolution/contrast.dat IN ../../data/evolution/contrast.tree IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI contrast.fcontrast FC = 19 FP /^ 3.9423 1.7028\n/ FP /^ 1.0000 0.4319\n/ FP /^ 1.0000 0.6566\n/ FI stdout FC = 5 FP 2 /^./ // ID fcontrast-reg AB phylipnew AA fcontrast CL -reg CC The -reg option is not yet giving the expected results CC when compared to phylip 3.6 IN ../../data/evolution/contrast.dat IN ../../data/evolution/contrast.tree IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI contrast.fcontrast FC = 27 FP /^ 3.35832 0.89706\n/ FP /^ 1.0000 0.4319\n/ FP /^ 1.0000 0.6566\n/ FI stdout FC = 7 FP 3 /^./ // ID fdiscboot-ex AB phylipnew AA fdiscboot CL -seed 3 IN ../../data/evolution/discboot.dat IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ FI discboot.ancfile FZ = 0 FI discboot.factfile FZ = 0 FI discboot.mixfile FZ = 0 FI discboot.fdiscboot FC = 600 FP 100 /^Alpha/ FP 10 /^Alpha 111100\n/ // ID fdnacomp-ex AB phylipnew AA fdnacomp CL -ancseq -stepbox -printdata IN ../../data/evolution/dnacomp.dat IN IN IN FI dnacomp.fdnacomp FC = 62 FP /total number of compatible sites is 11.0\n/ FP / 4 Epsilon maybe GGGATCTCGG CCC\n/ FP / 0[|] 2 1 3 2 0 2 1 1 1\n/ FP / 0 [!] YYNYYYYYY\n/ FP /One most parsimonious tree found:\n/ FI dnacomp.treefile FC = 1 FP /\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 11 /^./ // ID fdnacomp-ex2 AB phylipnew AA fdnacomp IN ../../data/evolution/dnacomp.dat IN ../../data/evolution/dnacomptree.dat IN IN FI dnacomp.fdnacomp FC = 23 FP /^User-defined tree:\n/ FP /^total number of compatible sites is 11.0\n/ FI dnacomp.treefile FC = 1 FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP 2 /^./ // ID fdnadist-ex AB phylipnew AA fdnadist IN ../../data/evolution/dnadist.dat IN IN FI dnadist.fdnadist FC = 9 FP / 5\n/ FP /^Alpha 0.000000 0.303893 0.857546 1.158921 1.542897\n/ FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 11 FP 8 /^./ // ID fdnainvar-ex AB phylipnew AA fdnainvar CL -printdata IN ../../data/evolution/dnainvar.dat IN IN FI dnainvar.fdnainvar FC = 120 FP /^ AAAG 2\n/ FP /^ 1113 3\n/ FP /^ III: \(\(Alpha,Delta\),\(Beta,Gamma\)\)\n/ FP /^ III 0 - 0 = 0 1.0000 no\n/ FP /^ Quadratic invariant = 4.0\n/ FP 3 /^ Quadratic invariant =/ FP / Tree III: 5.0\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID fdnaml-ex AB phylipnew AA fdnaml CL -printdata CL -ncategories 2 -categories "1111112222222" -rate "1.0 2.0" CL -gamma h CL -nhmmcategories 5 -hmmrates "0.264 1.413 3.596 7.086 12.641" CL -hmmprobabilities "0.522 0.399 0.076 0.0036 0.000023" CL -lambda 1.5 CL -weight "0111111111110" IN ../../data/evolution/dnaml.dat IN IN FI dnaml.fdnaml FC = 90 FP /^ 1 0.264 0.522\n/ FP /^ 2 2.000\n/ FP /^Ln Likelihood = -57.89164\n/ FP /^ +2 + Alpha +0.26902 +\( +zero, +0.80593\) \*\n/ FP /^ 1132121111 211\n/ FI dnaml.treefile FC = 2 FP /^\(\(Epsilon:0.13647,Delta:0.13781\):7.83947,\(Gamma:0.95525,\n/ FP /^Beta:0.04509\):0.00006,Alpha:0.26902\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 54 FP 45 /^./ // ID fdnaml-ex2 AB phylipnew AA fdnaml CL -printdata CL -njumble 3 -seed 3 IN ../../data/evolution/dnaml.dat IN IN FI dnaml.fdnaml FC = 56 FP /^ A 0.24615\n/ FP /^Ln Likelihood = -72.25088\n/ FP /^ 1 Epsilon 0\.00006 \( zero, 0\.34299\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 68 FP 57 /^./ FI dnaml.treefile FC = 2 FP /^Gamma:1.01654,Alpha:0.20753\);\n/ // ID fdnamlk-ex AB phylipnew AA fdnamlk CL -printdata CL -ncategories 2 -categories "1111112222222" -rate "1.0 2.0" CL -gamma h CL -nhmmcategories 5 -hmmrates "0.264 1.413 3.596 7.086 12.641" CL -hmmprobabilities "0.522 0.399 0.076 0.0036 0.000023" CL -lambda 1.5 CL -weight "0111111111110" IN ../../data/evolution/dnaml.dat IN IN FI dnaml.fdnamlk FC = 89 FP /^ 1 0.264 0.522\n/ FP /^ 2 2.000\n/ FP /^Ln Likelihood = -60.787[0-9][0-9]\n/ FP /^ +2 +Gamma +4.52951 +0.90802\n/ FP /^ 1121121111 111\n/ FI dnaml.treefile FC = 2 FP /^\(\(Epsilon:0.58158,Delta:0.58158\):3.94793,\(Gamma:0.90802,\n/ FP /^\(Beta:0.67882,Alpha:0.67882\):0.22921\):3.62149\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 55 FP 47 /^./ // ID fdnamove-ex AB phylipnew AA fdnamove IN ../../data/evolution/dnamove.dat IN IN Q IN Y FI dnamove.treefile FC = 1 FP /^\(Epsilon,\(Delta,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 20 FP 14 /^./ // ID fdnapars-ex AB phylipnew AA fdnapars IN ../../data/evolution/dnapars.dat IN IN FI dnapars.fdnapars FC = 30 FP /^requires a total of 19.000\n/ FP /^ 3 Epsilon 0.096154\n/ FI dnapars.treefile FC = 2 FP /^\(\(\(Epsilon:0.09615,Delta:0.13462\):0.48718,Gamma:0.27564\):0.21795,\n/ FP /^Beta:0.07692,Alpha:0.17308\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 21 FP 15 /^./ // ID fdnapenny-ex AB phylipnew AA fdnapenny IN ../../data/evolution/dnapenny.dat IN FI dnapenny.fdnapenny FC = 207 FP /^ 9 trees in all found\n/ FP /^ \! \+-----6 \+-----Gamma2 \n/ FI dnapenny.treefile FC = 9 FP /^\(Alpha1,\(\(\(\(\(Delta,Epsilon\),Gamma2\),Gamma1\),\(Beta2,Beta1\)\),Alpha2\)\)\[0.1111\];\n/ FP 3 /\(Gamma2,Gamma1\)/ FP 9 /\(Delta,Epsilon\),/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 11 /^./ // ID fdollop-ex AB phylipnew AA fdollop IN ../../data/evolution/dollop.dat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dollop.fdollop FC = 24 FP /^One most parsimonious tree found:\n/ FP 1 /^requires a total of 3.000\n/ FI dollop.treefile FC = 1 FP /^\(Delta,\(Epsilon,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stdout FC = 18 FP 12 /^./ // ID fdolmove-ex AB phylipnew AA fdolmove IN ../../data/evolution/dolmove.dat IN IN Q IN Y FI dolmove.treefile FC = 1 FP /^\(Epsilon,\(Delta,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 24 FP 15 /^./ // ID fdolpenny-ex AB phylipnew AA fdolpenny IN ../../data/evolution/dolpenny.dat IN FI dolpenny.fdolpenny FC = 63 FP /^ 3 trees in all found\n/ FP 1 /^ \+--6 \+--5 \n/ FI dolpenny.treefile FC = 3 FP /^\(Delta,\(Epsilon,\(Gamma1,\(Alpha2,\(\(Beta2,Beta1\),Alpha1\)\)\)\)\)\[0.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(Beta2,Beta1\),\(Alpha2,Alpha1\)\)\)\)\)\[0.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(\(Beta2,Beta1\),Alpha2\),Alpha1\)\)\)\)\[0.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 13 FP 9 /^./ // ID fdrawgram-ex AB phylipnew AA fdrawgram CL -previewer n IN ../../data/evolution/drawgram.tree IN IN Y FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 12 FP 8 /^./ FI drawgram.fdrawgram FC = 76 FP /\%\!PS-Adobe-2.0\n/ FP 5 /show\n/ // ID fdrawtree-ex AB phylipnew AA fdrawtree IN ../../data/evolution/drawgram.tree IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 12 FP 8 /^./ FI drawgram.fdrawtree FC = 86 FP /\%\!PS-Adobe-2.0\n/ FP 5 /show\n/ // ID ffactor-ex AB phylipnew AA ffactor CC output fails to match documentation, also reports failure IN ../../data/evolution/factor.dat IN FI factor.ffactor FC = 5 FP /^ +4 +8\n/ FP /^Alpha 11100000\n/ FP /^Beta 10001001\n/ FP /^Gamma 00011100\n/ FP /^Epsilon 11101010\n/ FI factor.factor FC = 0 FI factor.ancestor FC = 0 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ffitch-ex AB phylipnew AA ffitch IN ../../data/evolution/fitch.dat IN IN FI fitch.ffitch FC = 50 FP /^ 7 Populations\n/ FP /^Sum of squares = 0.01375\n/ FP /^Average percent standard deviation = 1.85418\n/ FP /^ 1 Mouse 0.76985\n/ FP /^ 1 2 0.41983\n/ FP /^ 2 Gibbon 0.35537\n/ FI fitch.treefile FC = 2 FP /^\(Mouse:0.76985,\(\(\(\(Human:0.11449,Chimp:0.15471\):0.03695,\n/ FP /^Gorilla:0.15680\):0.02121,Orang:0.29209\):0.04986,Gibbon:0.35537\):0.41983,Bovine:0.91675\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 57 FP 52 /^./ // ID ffreqboot-ex AB phylipnew AA ffreqboot CL -seed 3 IN ../../data/evolution/freqboot.dat IN FI freqboot.ffreqboot FC = 1700 FP 100 /^European/ FP 57 /^European 0.28680 / FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID fgendist-ex AB phylipnew AA fgendist IN ../../data/evolution/gendist.dat IN FI gendist.fgendist FC = 6 FP /^ 5\n/ FP /^Chinese 0.080749 0.234698 0.000000 0.053879 0.063275\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 11 FP 8 /^./ // ID fkitsch-ex AB phylipnew AA fkitsch IN ../../data/evolution/kitsch.dat IN IN FI kitsch.fkitsch FC = 49 FP /^ 7 Populations\n/ FP /^Sum of squares = 0.107\n/ FP /^Average percent standard deviation = 5.16213\n/ FP /^ 6 Human 0.13460 0.81285\n/ FP /^ 5 6 0.02836 0.67825\n/ FP /^ 6 Chimp 0.13460 0.81285\n/ FI kitsch.treefile FC = 3 FP /^\(\(\(\(\(\(Human:0.13460,Chimp:0.13460\):0.02836,Gorilla:0.16296\):0.07638,\n/ FP /^Orang:0.23933\):0.06639,Gibbon:0.30572\):0.42923,Mouse:0.73495\):0.07790,\n/ FP /^Bovine:0.81285\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 61 FP 55 /^./ // ID fmix-ex AB phylipnew AA fmix IN ../../data/evolution/mix.dat IN IN FI mix.fmix FC = 86 FP 4 /^requires a total of 9.000\n/ FP /^ 4 trees in all found\n/ FP 2 /^--1 \! \+--Delta +\n/ FI mix.treefile FC = 4 FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0.2500\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.2500\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0.2500\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0.2500\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 16 FP 11 /^./ // ID fmix-ex2 AB phylipnew AA fmix CL -printdata -ancfile ../../data/evolution/mixancfile.dat IN ../../data/evolution/mix.dat IN IN FI mix.fmix FC = 46 FP /^ Ancestral states:\n/ FP /^ 001\?\? 1\n/ FP /^One most parsimonious tree found:\n/ FP /^requires a total of 8.000\n/ FI mix.treefile FC = 1 FP /^\(Delta,\(Epsilon,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 16 FP 11 /^./ // ID fmove-ex AB phylipnew AA fmove IN ../../data/evolution/move.dat IN IN Q IN Y FI move.treefile FC = 1 FP /^\(Epsilon,\(Delta,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 15 /^./ // ID fneighbor-ex AB phylipnew AA fneighbor IN ../../data/evolution/neighbor.dat IN FI neighbor.fneighbor FC = 43 FP /^ 7 Populations\n/ FP /^ \! \! \+--------Gorilla \n/ FP /^ 1 Mouse 0.76891\n/ FP /^ 1 2 0.42027\n/ FP /^ 2 Gibbon 0.35793\n/ FI neighbor.treefile FC = 2 FP /^\(Mouse:0.76891,\(Gibbon:0.35793,\(Orang:0.28469,\(Gorilla:0.15393,\n/ FP /^\(Chimp:0.15168,Human:0.11752\):0.03982\):0.02696\):0.04648\):0.42027,Bovine:0.91769\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 38 FP 32 /^./ // ID fpars-ex AB phylipnew AA fpars IN ../../data/evolution/pars.dat IN IN FI pars.fpars FC = 30 FP /^One most parsimonious tree found:\n/ FP /^requires a total of 8.000\n/ FP /^ 3 Epsilon 0.00\n/ FP /^ 3 Delta 3.00\n/ FI pars.treefile FC = 1 FP /^\(\(\(Epsilon:0.00,Delta:3.00\):2.00,Gamma:0.00\):1.00,Beta:2.00,Alpha:0.00\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 21 FP 15 /^./ // ID fpenny-ex AB phylipnew AA fpenny IN ../../data/evolution/penny.dat IN FI penny.fpenny FC = 70 FP /^ 3 trees in all found\n/ FP 3 /^ remember: this is an unrooted tree\!\n/ FP /^ \! \+-----Alpha2 \n/ FI penny.treefile FC = 3 FP /^\(Alpha1,\(\(Alpha2,\(\(Epsilon,Delta\),Gamma1\)\),\(Beta2,Beta1\)\)\)\[0.3333\];\n/ FP /^\(Alpha1,\(Alpha2,\(\(\(Epsilon,Delta\),Gamma1\),\(Beta2,Beta1\)\)\)\)\[0.3333\];\n/ FP /^\(Alpha1,\(\(Alpha2,\(Beta2,Beta1\)\),\(\(Epsilon,Delta\),Gamma1\)\)\)\[0.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 16 FP 12 /^./ // ID fproml-ex AB phylipnew AA fproml IN ../../data/evolution/proml.dat IN IN FI proml.fproml FC = 33 FP /^Ln Likelihood = -131.58633\n/ FP /^ 1------2 \+------------Delta \n/ FP /^ 1 +Alpha +0.30915 +\( +zero, +0.66607\) \*\*\n/ FI proml.treefile FC = 2 FP /^\(Beta:0.00010,\(\(Epsilon:0.00010,Delta:0.41008\):1.00021,\n/ FP /^Gamma:0.68318\):0.22118,Alpha:0.30915\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 9 /^./ // ID fpromlk-ex AB phylipnew AA fpromlk IN ../../data/evolution/promlk.dat IN IN FI promlk.fpromlk FC = 38 FP /^Ln Likelihood = -134.75201\n/ FP /^ root 3 \n/ FP /^ 3 4 0.66099 0.66099\n/ FP /^ 4 Epsilon 0.85359 0.19260\n/ FI promlk.treefile FC = 2 FP /^\(\(Epsilon:0.19260,Delta:0.19260\):0.66099,\(Gamma:0.48440,\n/ FP /^\(Beta:0.15708,Alpha:0.15708\):0.32732\):0.36919\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 19 FP 11 /^./ // ID fprotdist-ex AB phylipnew AA fprotdist IN ../../data/evolution/protdist.dat IN FI protdist.fprotdist FC = 9 FP /^Gamma 0.625670 0.375578 0.000000 0.975798 0.861634\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 30 FP 27 /^./ // ID fprotpars-ex AB phylipnew AA fprotpars IN ../../data/evolution/protpars.dat IN IN FI protpars.fprotpars FC = 61 FP /^ 3 trees in all found\n/ FP 1 /^ \! \+--Beta \n/ FP 2 /^ \! +\+-+Beta +\n/ FI protpars.treefile FC = 3 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 16 FP 11 /^./ // ID fprotpars-ex2 AB phylipnew AA fprotpars CL -njumble 3 -seed 3 CL -printdata CL -ancseq CL -whichcode m CL -stepbox CL -outgrno 2 CL -thresh -threshold 3 IN ../../data/evolution/protpars.dat IN IN FI protpars.fprotpars FC = 137 FP /^ 3 trees in all found\n/ FP 3 /^requires a total of 14.000\n/ FI protpars.treefile FC = 3 FP /^\(Beta,\(Gamma,\(\(Epsilon,Delta\),Alpha\)\)\)\[0.3333\];\n/ FP /^\(Beta,\(\(\(Epsilon,Delta\),Gamma\),Alpha\)\)\[0.3333\];\n/ FP /^\(Beta,\(\(Epsilon,Delta\),\(Gamma,Alpha\)\)\)\[0.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 40 FP 29 /^./ // ID fprotpars-ex3 AB phylipnew AA fprotpars CL -njumble 3 -seed 3 IN ../../data/evolution/protpars2.dat IN IN FI protpars2.fprotpars FC = 435 FP /^Data set # 1:\n/ FP /^ 3 trees in all found\n/ FP 3 /^requires a total of 25.000\n/ FP /^Data set # 2:\n/ FP /^ 15 trees in all found\n/ FP 15 /^requires a total of 14.000\n/ FP /^Data set # 3:\n/ FP /^ 5 trees in all found\n/ FP 5 /^requires a total of 24.000\n/ FI protpars2.treefile FC = 23 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0.3333\];\n/ FP /^\(\(Gamma,\(Delta,\(Epsilon,Beta\)\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(\(Delta,Gamma\),\(Epsilon,Beta\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(\(Delta,\(Epsilon,Gamma\)\),Beta\),Alpha\)\[0.0667\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0.0667\];\n/ FP /^\(\(Epsilon,\(\(Delta,Gamma\),Beta\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(\(Epsilon,\(Delta,Gamma\)\),Beta\),Alpha\)\[0.0667\];\n/ FP /^\(\(Delta,\(Gamma,\(Epsilon,Beta\)\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(Delta,\(\(Epsilon,Gamma\),Beta\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(Delta,\(Epsilon,\(Gamma,Beta\)\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(Epsilon,\(Delta,\(Gamma,Beta\)\)\),Alpha\)\[0.0667\];\n/ FP /^\(\(Gamma,\(Delta,\(Epsilon,Beta\)\)\),Alpha\)\[0.2000\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.2000\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0.2000\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0.2000\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0.2000\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 126 FP 90 /^./ // ID fprotpars-ex4 AB phylipnew AA fprotpars CL -option IN ../../data/evolution/protpars.dat IN IN ../../data/evolution/protparswts.dat IN IN IN IN IN IN IN IN IN IN IN IN FI protpars.fprotpars FC = 324 FP /^Weights set # 1:\n/ FP /^ 3 trees in all found\n/ FP 3 /^requires a total of 14.000\n/ FP /^Weights set # 2:\n/ FP /^ 14 trees in all found\n/ FP 14 /^requires a total of 2.000\n/ FI protpars.treefile FC = 17 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0.3333\];\n/ FP /^\(\(Gamma,\(Delta,\(Epsilon,Beta\)\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(\(Delta,Gamma\),\(Epsilon,Beta\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(\(Delta,\(Epsilon,Gamma\)\),Beta\),Alpha\)\[0.0714\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0.0714\];\n/ FP /^\(\(Epsilon,\(\(Delta,Gamma\),Beta\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(\(Epsilon,\(Delta,Gamma\)\),Beta\),Alpha\)\[0.0714\];\n/ FP /^\(\(Delta,\(Gamma,\(Epsilon,Beta\)\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(Delta,\(\(Epsilon,Gamma\),Beta\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(Delta,\(Epsilon,\(Gamma,Beta\)\)\),Alpha\)\[0.0714\];\n/ FP /^\(\(Epsilon,\(Delta,\(Gamma,Beta\)\)\),Alpha\)\[0.0714\];\n/ FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 38 FP 24 /^./ // ID frestboot-ex AB phylipnew AA frestboot CL -seed 3 IN ../../data/evolution/restboot.dat IN FI restboot.frestboot FC = 600 FP 100 /^Gamma/ FP 3 /^Gamma \-\+\-\-\-\+\+\+\+\+\ \+\+\+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID frestdist-ex AB phylipnew AA frestdist IN ../../data/evolution/restdist.dat IN FI restdist.frestdist FC = 6 FP /^Gamma 0.107681 0.107681 0.000000 0.176484 0.192466\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 14 FP 9 /^./ // ID frestml-ex AB phylipnew AA frestml IN ../../data/evolution/restml.dat IN IN FI restml.frestml FC = 41 FP /^Ln Likelihood = -40.34358\n/ FP /^ 1 +Gamma +0.10813 \( 0.01154, 0.21901\) \*\*\n/ FI restml.treefile FC = 2 FP /^\(Gamma:0.10813,\(\(Epsilon:0.00100,Delta:0.01460\):0.05885,\n/ FP /^Beta:0.00100\):0.01156,Alpha:0.01310\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 10 /^./ // ID fretree-ex AB phylipnew AA fretree CC First prompt only needed until it can read CC the number of species from the input tree IN 10 IN ../../data/evolution/retree.dat IN IN Q IN Y IN U FI retree.treefile FC = 2 FP /^\(\(\(\(\(\(\(Human,Chimp\),Gorilla\),Orang\),Gibbon\),\(Barbary_Ma,\(Crab-e._Ma,\n/ FP /^\(Rhesus_Mac,Jpn_Macaq\)\)\)\),Squir._Mon\),\(\(Tarsier,Lemur\),Bovine\),Mouse\);\n/ FI stderr FC = 4 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 27 FP 23 /^./ // ID fseqboot-ex AB phylipnew AA fseqboot CL -seed 3 IN ../../data/evolution/seqboot.dat IN FI seqboot.fseqboot FC = 600 FP 7 /^Alpha AAAAAA\n/ FP 14 /^Beta AAACCC\n/ FP 21 /^\S+ +AAACCC\n/ FP 100 /^Alpha/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID fseqbootall-ex AB phylipnew AA fseqbootall CL -seed 3 IN ../../data/evolution/seqboot.dat IN FI seqboot.fseqbootall FC = 600 FP 7 /^Alpha AAAAAA\n/ FP 14 /^Beta AAACCC\n/ FP 21 /^\S+ +AAACCC\n/ FP 100 /^Alpha/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID ftreedist-ex AB phylipnew AA ftreedist IN ../../data/evolution/treedist.dat IN FI treedist.ftreedist FC = 11 FP /Trees 1 and 2: 4/ FP 6 /Trees \d+ and \d+:\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedist-ex2 AB phylipnew AA ftreedist CL -dtype s IN ../../data/evolution/treedist2.dat IN FI treedist2.ftreedist FC = 11 FP /Trees 1 and 2: 4/ FP 6 /Trees \d+ and \d+:\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedist-sparse AB phylipnew AA ftreedist CL -style s IN ../../data/evolution/treedist.dat IN IN FI treedist.ftreedist FC = 6 FP /1 2 4/ FP 6 /\d+\s+\d+\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedist-listall AB phylipnew AA ftreedist CL -dtype s IN ../../data/evolution/treedist.dat IN FI treedist.ftreedist FC = 11 FP /Trees 11 and 12: 10\n/ FP 6 /Trees \d+ and \d+:\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedistpair-ex AB phylipnew AA ftreedistpair CL -style s IN ../../data/evolution/treedist.dat IN ../../data/evolution/treedist.dat IN FI treedist.ftreedistpair FC = 288 FP /^1 14 4.000000e-02\n/ FP /^2 13 4.000000e-02\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP 1 /^./ // ####################################### # TOPO ####################################### ID topo-ex AB topo AA topo CL tsw:aqp1_human -signa -prol=UM -cys=cg -gly=sr -acid=dr CL -basic=db -ohaa=da -araa=dg -graph ps IN 18 35 49 67 94 115 136 156 165 184 211 232 IN n IN 74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Created topo.ps\n/ FI topo.ps FZ > 950000 FP /^%%Title: PLplot Graph\n/ // ####################################### # APPENDIXD ####################################### ID crystalball-ex AB appendixd AA crystalball CL -competition -rdtime -rdcost -animalstudies -clinicaltrials CL -fdaproblems -fdatime -profit -everythingelse IN tembl:hsfau IN FI hsfau.crystalball FC = 9 FP 9 /:/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 //