# HG changeset patch # User cschu # Date 1427880952 14400 # Node ID 4fdaf732231a0b6acb262af4fce0a6a0e665ec98 # Parent a512d17b12c9f4f83af94b0450fd1ec074d4a897 Deleted selected files diff -r a512d17b12c9 -r 4fdaf732231a synteny_parse.py --- 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:]) diff -r a512d17b12c9 -r 4fdaf732231a synteny_parse.xml --- 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 @@ - - Parse synteny information from BlastXML. - - - biopython - Bio - Bio.Blast - - synteny_parse.py - --evalue="${minE.value}" - --min-identity="${minID.value}" - --min-query-coverage="${minQCOV.value}" - $blastXML_in $out - - - - - - - amino acid sequences" /> - - - - - - - This tool does stuff. - - - diff -r a512d17b12c9 -r 4fdaf732231a tool_dependencies.xml --- 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 @@ - - - - - -