Mercurial > repos > peterjc > seq_composition
changeset 2:4283011f4be2 draft
v0.0.3 Internal Python style updates
| author | peterjc |
|---|---|
| date | Wed, 01 Feb 2017 10:00:22 -0500 |
| parents | c0eb0e5792f3 |
| children | 7a26bb458806 |
| files | tools/seq_composition/README.rst tools/seq_composition/seq_composition.py tools/seq_composition/seq_composition.xml tools/seq_composition/tool_dependencies.xml |
| diffstat | 4 files changed, 14 insertions(+), 18 deletions(-) [+] |
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--- a/tools/seq_composition/README.rst Wed May 13 10:49:27 2015 -0400 +++ b/tools/seq_composition/README.rst Wed Feb 01 10:00:22 2017 -0500 @@ -1,7 +1,7 @@ Galaxy tool reporting sequence composition ========================================== -This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute +This tool is copyright 2014-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -60,6 +60,7 @@ - Tool definition now embeds citation information. v0.0.2 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.0.3 - Python style updates (internal change only). ======= ====================================================================== @@ -74,12 +75,12 @@ 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):: - $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ ... or:: - $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ ... To just build and check the tar ball, use::
--- a/tools/seq_composition/seq_composition.py Wed May 13 10:49:27 2015 -0400 +++ b/tools/seq_composition/seq_composition.py Wed Feb 01 10:00:22 2017 -0500 @@ -15,17 +15,12 @@ Use -v or --version to get the version, -h or --help for help. """ -import os import sys from optparse import OptionParser from Bio import SeqIO -def sys_exit(msg, err=1): - sys.stderr.write(msg.rstrip() + "\n") - sys.exit(err) - -#Parse Command Line +# Parse Command Line usage = """Example usage: $ python seq_composition.py -o my_output.tsv -q input1.fastq -q input2.fastq @@ -34,9 +29,9 @@ If the expected alphabet is given, the sequence composition is verfied against it. """ -#TODO - Case senstivity? -#TODO - GenBank / EMBL input? Needs the datatype defined... -#TODO - Handle all the FASTQ datatype subclasses in the XML cheetah code? +# TODO - Case senstivity? +# TODO - GenBank / EMBL input? Needs the datatype defined... +# TODO - Handle all the FASTQ datatype subclasses in the XML cheetah code? parser = OptionParser(usage=usage) parser.add_option('-f', '--fasta', dest='fasta', action="append", default=[], help='Input sequence filename in FASTA format') @@ -54,13 +49,13 @@ options, args = parser.parse_args() if options.version: - print("v0.0.1") + print("v0.0.3") sys.exit(0) if not (options.fasta or options.fastq or options.sff): - sys_exit("Require an input filename") + sys.exit("Requires an input filename") if not options.output: - sys_exit("Require an output filename") + sys.exit("Requires an output filename") file_count = 0 @@ -78,7 +73,7 @@ for letter in record: try: counts[letter] += 1 - except: + except KeyError: counts[letter] = 1 total = sum(counts.values())
--- a/tools/seq_composition/seq_composition.xml Wed May 13 10:49:27 2015 -0400 +++ b/tools/seq_composition/seq_composition.xml Wed Feb 01 10:00:22 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="seq_composition" name="Sequence composition" version="0.0.2"> +<tool id="seq_composition" name="Sequence composition" version="0.0.3"> <description>Count bases or amino-acids</description> <requirements> <requirement type="package" version="1.64">biopython</requirement>
--- a/tools/seq_composition/tool_dependencies.xml Wed May 13 10:49:27 2015 -0400 +++ b/tools/seq_composition/tool_dependencies.xml Wed Feb 01 10:00:22 2017 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.64"> - <repository changeset_revision="5477a05cc158" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0c7526e8ea70" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>