Mercurial > repos > cschu > cs_test_me
changeset 1:4fdaf732231a draft
Deleted selected files
| author | cschu |
|---|---|
| date | Wed, 01 Apr 2015 05:35:52 -0400 |
| parents | a512d17b12c9 |
| children | ea73705ac0f6 |
| files | synteny_parse.py synteny_parse.xml tool_dependencies.xml |
| diffstat | 3 files changed, 0 insertions(+), 99 deletions(-) [+] |
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--- a/synteny_parse.py Wed Apr 01 05:34:17 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import argparse - -#from Bio import Blast - -from Bio.Blast import NCBIXML -# from Blast import NCBIXML - - -def doStuff(args): - blast_records = NCBIXML.parse(open(args.blastXMLInput)) - - with open(args.blastHitsTSV, 'wb') as out: - for blast_record in blast_records: - qlen = blast_record.query_length - qid = blast_record.query - # hits[qid] = [] - for alignment in blast_record.alignments: - sid = alignment.title.split()[1] - tid = sid.split('|')[0] - for hsp in alignment.hsps: - if hsp.expect >= args.evalue: - continue - qcov = (hsp.query_end - hsp.query_start + 1.0) / qlen - if qcov < args.min_query_coverage: - continue - identity = hsp.identities / float(hsp.align_length) - if identity < args.min_identity: - continue - - hit = (tid, sid, hsp.expect, qcov, qlen, hsp.align_length, identity) - out.write('\t'.join([qid] + map(str, hit)) + '\n') - pass - - -def main(argv): - - descr = '' - parser = argparse.ArgumentParser(description=descr) - parser.add_argument('--evalue', type=float, default=1e-10) - parser.add_argument('--min-identity', type=float, default=0.75) - parser.add_argument('--min-query-coverage', type=float, default=0.75) - parser.add_argument('blastXMLInput', type=str) - parser.add_argument('blastHitsTSV', type=str) - - try: - args = parser.parse_args() - except: - sys.exit(1) - - if not os.path.exists(args.blastXMLInput): - sys.stderr.write('Input file (%s) is missing.\n' % args.blastXMLInput) - sys.exit(1) - - doStuff(args) - - pass - - -if __name__ == '__main__': main(sys.argv[1:])
--- a/synteny_parse.xml Wed Apr 01 05:34:17 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -<tool id="synteny_parse" name="synteny_parse"> - <description>Parse synteny information from BlastXML.</description> - <requirements> - <!-- <requirement type="package" version="2.7.4">python</requirement> --> - <requirement type="package" version="1.62">biopython</requirement> - <requirement type="python-module">Bio</requirement> - <requirement type="python-module">Bio.Blast</requirement> - </requirements> - <command interpreter="python">synteny_parse.py - --evalue="${minE.value}" - --min-identity="${minID.value}" - --min-query-coverage="${minQCOV.value}" - $blastXML_in $out - </command> - <inputs> - <param name="blastXML_in" type="data" format="xml" label="BLAST xml output" /> - <param name="minE" type="float" value="1e-10" label="e-value cutoff" /> - <param name="minID" type="float" value="0.75" label="identity cutoff" /> - <param name="minQCOV" type="float" value="0.75" label="query-coverage cutoff" /> - amino acid sequences" /> - </inputs> - <outputs> - <data format="tabular" name="out" label="Filtered Blast results ${on_string}" /> - </outputs> - - <help> - This tool does stuff. - </help> -</tool> -
--- a/tool_dependencies.xml Wed Apr 01 05:34:17 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="biopython" version="1.65"> - <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>