# 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 @@
-
-
-
-
-
-