Mercurial > repos > peterjc > seq_filter_by_id
changeset 14:fa920e4c3463 draft
Uploaded v0.2.0 preview 1, fixed Biopython dependency declaration
| author | peterjc |
|---|---|
| date | Wed, 30 Jul 2014 06:37:38 -0400 |
| parents | 97151ae9eb2b |
| children | a6cb323413c0 |
| files | tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.py tools/seq_filter_by_id/seq_filter_by_id.tar.gz tools/seq_filter_by_id/seq_filter_by_id.xml tools/seq_filter_by_id/tool_dependencies.xml |
| diffstat | 5 files changed, 16 insertions(+), 10 deletions(-) [+] |
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--- a/tools/seq_filter_by_id/README.rst Wed Jun 11 11:25:26 2014 -0400 +++ b/tools/seq_filter_by_id/README.rst Wed Jul 30 06:37:38 2014 -0400 @@ -76,6 +76,7 @@ v0.2.0 - Can supply ID list as a text parameter (instead of in a file) - Using optparse for command line API. - Advanced option to ignore paired read suffices. + - Updated dependencies to use Biopython 1.64. ======= ======================================================================
--- a/tools/seq_filter_by_id/seq_filter_by_id.py Wed Jun 11 11:25:26 2014 -0400 +++ b/tools/seq_filter_by_id/seq_filter_by_id.py Wed Jul 30 06:37:38 2014 -0400 @@ -29,7 +29,7 @@ (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. See accompanying text file for licence details (MIT license). -This is version 0.2.0 of the script, use -v or --version to get the version. +Use -v or --version to get the version, -h or --help for help. """ import os import sys @@ -40,10 +40,6 @@ sys.stderr.write(msg.rstrip() + "\n") sys.exit(err) -if "-v" in sys.argv or "--version" in sys.argv: - print "v0.2.0" - sys.exit(0) - #Parse Command Line usage = """Use as follows: @@ -79,7 +75,16 @@ parser.add_option("-s", "--suffix", dest="suffix", action="store_true", help="Ignore pair-read suffices for matching names") -(options, args) = parser.parse_args() +parser.add_option("-v", "--version", dest="version", + default=False, action="store_true", + help="Show version and quit") + +options, args = parser.parse_args() + +if options.version: + print "v0.2.0" + sys.exit(0) + in_file = options.input seq_format = options.format out_positive_file = options.output_positive
--- a/tools/seq_filter_by_id/seq_filter_by_id.xml Wed Jun 11 11:25:26 2014 -0400 +++ b/tools/seq_filter_by_id/seq_filter_by_id.xml Wed Jul 30 06:37:38 2014 -0400 @@ -1,7 +1,7 @@ <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.0"> <description>from a tabular file</description> <requirements> - <requirement type="package" version="1.63">biopython</requirement> + <requirement type="package" version="1.64">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> <version_command interpreter="python">seq_filter_by_id.py --version</version_command> @@ -154,7 +154,7 @@ or just the non-matching ones. Instead of providing the identifiers in a tabular file, you can alternatively -provide them as a paramter (type or paste them into the text box). This is a +provide them as a parameter (type or paste them into the text box). This is a useful shortcut for extracting a few sequences of interest without first having to prepare a tabular file.
--- a/tools/seq_filter_by_id/tool_dependencies.xml Wed Jun 11 11:25:26 2014 -0400 +++ b/tools/seq_filter_by_id/tool_dependencies.xml Wed Jul 30 06:37:38 2014 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.62"> - <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.64"> + <repository changeset_revision="268128adb501" name="package_biopython_1_64" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>