# HG changeset patch # User peterjc # Date 1431514666 14400 # Node ID d0d604b9ab9a60924119d64a4fa1161744338803 # Parent e12fd6f5992c70f4a0b41794aba0a816393c1349 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/seq_primer_clip commit d9d02b01e942b3a7a3a13a85579ab16c17e9c459 diff -r e12fd6f5992c -r d0d604b9ab9a test-data/MID4_GLZRM4E04_rnd30.fasta --- a/test-data/MID4_GLZRM4E04_rnd30.fasta Fri Nov 28 11:49:37 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ ->GLZRM4E04IPVGX -CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ->GLZRM4E04I9EJK -CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ->GLZRM4E04JHW0A -TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ->GLZRM4E04IBNFY -CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ->GLZRM4E04IKCQP -CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ->GLZRM4E04ITXFU -CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT ->GLZRM4E04JAY4Z -CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ->GLZRM4E04H9M21 -CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ->GLZRM4E04IQDP5 -CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG ->GLZRM4E04I0CYE -TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT ->GLZRM4E04I2NA7 -CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA ->GLZRM4E04I5BWJ -CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC ->GLZRM4E04IK8WX -GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG ->GLZRM4E04I22QH -CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ->GLZRM4E04IVVFA -GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG ->GLZRM4E04ILU3V -CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ->GLZRM4E04IDVJT -CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG ->GLZRM4E04I3ZJ6 -CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG ->GLZRM4E04I3UBT -CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA ->GLZRM4E04H59S1 -CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ->GLZRM4E04JFA38 -CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT ->GLZRM4E04J4EK3 -CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG ->GLZRM4E04IK96G -CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA ->GLZRM4E04JVL8Q -CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT ->GLZRM4E04IOQ36 -CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT ->GLZRM4E04JBJJ1 -CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG ->GLZRM4E04IEFNO -CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA ->GLZRM4E04JOT5I -CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG ->GLZRM4E04J4HNG -CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT ->GLZRM4E04JC544 -CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC diff -r e12fd6f5992c -r d0d604b9ab9a test-data/MID4_GLZRM4E04_rnd30.sff Binary file test-data/MID4_GLZRM4E04_rnd30.sff has changed diff -r e12fd6f5992c -r d0d604b9ab9a test-data/MID4_GLZRM4E04_rnd30_fclip.pair_sample_N5.sff Binary file test-data/MID4_GLZRM4E04_rnd30_fclip.pair_sample_N5.sff has changed diff -r e12fd6f5992c -r d0d604b9ab9a test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff has changed diff -r e12fd6f5992c -r d0d604b9ab9a test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff has changed diff -r e12fd6f5992c -r d0d604b9ab9a test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular --- a/test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular Fri Nov 28 11:49:37 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -Letter Count Percentage -A 1733 27.68 -C 1267 20.24 -G 1551 24.78 -T 1709 27.30 diff -r e12fd6f5992c -r d0d604b9ab9a tools/seq_primer_clip/README.rst --- a/tools/seq_primer_clip/README.rst Fri Nov 28 11:49:37 2014 -0500 +++ b/tools/seq_primer_clip/README.rst Wed May 13 06:57:46 2015 -0400 @@ -1,7 +1,7 @@ Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads =========================================================== -This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -65,6 +65,9 @@ v0.0.11 - Correct automated dependency definition. v0.0.12 - Simplified XML to apply input format to output data. - Tool definition now embeds citation information. +v0.0.13 - Use ``format_source=...`` tag. + - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -78,19 +81,24 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: - $ tar -czf seq_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/tool_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30* +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: -Check this worked:: + $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ + ... - $ tar -tzf seq_primer_clip.tar.gz - tools/seq_primer_clip/README.rst - tools/seq_primer_clip/seq_primer_clip.xml - tools/seq_primer_clip/seq_primer_clip.py - tools/seq_primer_clip/tool_dependencies.xml - test-data/dop_primers.fasta +or:: + + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_primer_clip/ + ... + $ tar -tzf shed_upload.tar.gz test-data/MID4_GLZRM4E04_rnd30.fasta test-data/MID4_GLZRM4E04_rnd30.fastqsanger test-data/MID4_GLZRM4E04_rnd30_fclip.fasta @@ -100,6 +108,11 @@ test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30.sff + test-data/dop_primers.fasta + tools/seq_primer_clip/README.rst + tools/seq_primer_clip/seq_primer_clip.py + tools/seq_primer_clip/seq_primer_clip.xml + tools/seq_primer_clip/tool_dependencies.xml Licence (MIT) diff -r e12fd6f5992c -r d0d604b9ab9a tools/seq_primer_clip/seq_primer_clip.py --- a/tools/seq_primer_clip/seq_primer_clip.py Fri Nov 28 11:49:37 2014 -0500 +++ b/tools/seq_primer_clip/seq_primer_clip.py Wed May 13 06:57:46 2015 -0400 @@ -26,8 +26,8 @@ (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. See accompanying text file for licence details (MIT/BSD style). -This is version 0.0.8 of the script. Currently it uses Python's regular -expression engine for finding the primers, which for my needs is fast enough. +NOTE: Currently it uses Python's regular expression engine for finding the +primers, which for my needs is fast enough. """ import sys import re @@ -35,10 +35,10 @@ from galaxy_utils.sequence.fastq import fastqReader, fastqWriter if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.5" + print "v0.0.12" sys.exit(0) -def stop_err(msg, err=1): +def sys_exit(msg, err=1): sys.stderr.write(msg) sys.exit(err) @@ -46,7 +46,7 @@ from Bio.Seq import reverse_complement from Bio.SeqIO.SffIO import SffIterator, SffWriter except ImportError: - stop_err("Requires Biopython 1.54 or later") + sys_exit("Requires Biopython 1.54 or later") try: from Bio.SeqIO.SffIO import ReadRocheXmlManifest except ImportError: @@ -57,30 +57,30 @@ try: in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:] except ValueError: - stop_err("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) + sys_exit("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) if in_file == primer_fasta: - stop_err("Same file given as both primer sequences and sequences to clip!") + sys_exit("Same file given as both primer sequences and sequences to clip!") if in_file == out_file: - stop_err("Same file given as both sequences to clip and output!") + sys_exit("Same file given as both sequences to clip and output!") if primer_fasta == out_file: - stop_err("Same file given as both primer sequences and output!") + sys_exit("Same file given as both primer sequences and output!") try: mm = int(mm) except ValueError: - stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm) + sys_exit("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm) if mm < 0: - stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm) + sys_exit("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm) if mm not in [0,1,2]: raise NotImplementedError try: min_len = int(min_len) except ValueError: - stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len) + sys_exit("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len) if min_len < 0: - stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len) + sys_exit("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len) if keep_negatives.lower() in ["true", "yes", "on"]: @@ -88,7 +88,7 @@ elif keep_negatives.lower() in ["false", "no", "off"]: keep_negatives = False else: - stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives) + sys_exit("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives) if primer_type.lower() == "forward": @@ -101,7 +101,7 @@ forward = False rc = True else: - stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type) + sys_exit("Expected foward, reverse or reverse-complement not %r" % primer_type) ambiguous_dna_values = { @@ -281,7 +281,7 @@ negs += 1 writer.write(record) else: - short_negs += 1 + short_neg += 1 else: for record in reader: seq = record.sequence.upper() @@ -301,7 +301,7 @@ negs += 1 writer.write(record) else: - short_negs += 1 + short_neg += 1 elif seq_format.lower()=="fasta": in_handle = open(in_file, "rU") out_handle = open(out_file, "w") @@ -326,7 +326,7 @@ negs += 1 writer.write(record) else: - short_negs += 1 + short_neg += 1 else: for record in reader: seq = record.sequence.upper() @@ -345,9 +345,9 @@ negs += 1 writer.write(record) else: - short_negs += 1 + short_neg += 1 else: - stop_err("Unsupported file type %r" % seq_format) + sys_exit("Unsupported file type %r" % seq_format) in_handle.close() out_handle.close() diff -r e12fd6f5992c -r d0d604b9ab9a tools/seq_primer_clip/seq_primer_clip.xml --- a/tools/seq_primer_clip/seq_primer_clip.xml Fri Nov 28 11:49:37 2014 -0500 +++ b/tools/seq_primer_clip/seq_primer_clip.xml Wed May 13 06:57:46 2015 -0400 @@ -1,18 +1,18 @@ - + Trim off 5' or 3' primers biopython Bio - seq_primer_clip.py --version - -seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file - + seq_primer_clip.py --version + +seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file + @@ -28,7 +28,7 @@ - + @@ -86,9 +86,6 @@ - - Bio - **What it does**