Mercurial > repos > peterjc > seq_filter_by_id
changeset 2:abdd608c869b draft
Uploaded v0.0.5, checked script return code for errors X copes with a FASTA entry missing an ID.
| author | peterjc |
|---|---|
| date | Wed, 24 Apr 2013 11:34:12 -0400 |
| parents | 262f08104540 |
| children | 44ab4c0f7683 |
| files | tools/filters/seq_filter_by_id.py tools/filters/seq_filter_by_id.txt tools/filters/seq_filter_by_id.xml |
| diffstat | 3 files changed, 18 insertions(+), 4 deletions(-) [+] |
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--- a/tools/filters/seq_filter_by_id.py Mon Apr 15 12:27:30 2013 -0400 +++ b/tools/filters/seq_filter_by_id.py Wed Apr 24 11:34:12 2013 -0400 @@ -29,7 +29,7 @@ (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. See accompanying text file for licence details (MIT/BSD style). -This is version 0.0.4 of the script, use -v or --version to get the version. +This is version 0.0.5 of the script, use -v or --version to get the version. """ import sys @@ -38,7 +38,7 @@ sys.exit(err) if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.4" + print "v0.0.5" sys.exit(0) #Parse Command Line @@ -89,11 +89,18 @@ if line[0] == ">": break + no_id_warned = False while True: if line[0] != ">": raise ValueError( "Records in Fasta files should start with '>' character") - id = line[1:].split(None, 1)[0] + try: + id = line[1:].split(None, 1)[0] + except IndexError: + if not no_id_warned: + sys.stderr.write("WARNING - Malformed FASTA entry with no identifier\n") + no_id_warned = True + id = None lines = [line] line = handle.readline() while True:
--- a/tools/filters/seq_filter_by_id.txt Mon Apr 15 12:27:30 2013 -0400 +++ b/tools/filters/seq_filter_by_id.txt Wed Apr 24 11:34:12 2013 -0400 @@ -38,6 +38,8 @@ v0.0.4 - Record script version when run from Galaxy. - Faster FASTA code which preserves the original line wrapping. - Basic unit test included. +v0.0.5 - Check for errors using Python script's return code. + - Cope with malformed FASTA entries without an identifier. Developers
--- a/tools/filters/seq_filter_by_id.xml Mon Apr 15 12:27:30 2013 -0400 +++ b/tools/filters/seq_filter_by_id.xml Wed Apr 24 11:34:12 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.0.4"> +<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.0.5"> <description>from a tabular file</description> <version_command interpreter="python">seq_filter_by_id.py --version</version_command> <command interpreter="python"> @@ -11,6 +11,11 @@ - $output_neg #end if </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to filter on the identifiers" help="FASTA, FASTQ, or SFF format." /> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>