details: http://www.bx.psu.edu/hg/galaxy/rev/091573fd6e27 changeset: 1687:091573fd6e27 user: Nate Coraor nate@bx.psu.edu date: Mon Jan 05 15:26:17 2009 -0500 description: megablast fix from Anton
1 file(s) affected in this change:
tools/metag_tools/megablast_xml_parser.py
diffs (20 lines):
diff -r 696fc4c02a0c -r 091573fd6e27 tools/metag_tools/megablast_xml_parser.py --- a/tools/metag_tools/megablast_xml_parser.py Tue Dec 23 13:28:27 2008 -0500 +++ b/tools/metag_tools/megablast_xml_parser.py Mon Jan 05 15:26:17 2009 -0500 @@ -1,6 +1,6 @@ #! /usr/bin/python
-import sys, os +import sys, os, re
assert sys.version_info[:2] >= ( 2, 4 )
@@ -55,6 +55,8 @@ # for every <Hit> within <Iteration> for hit in elem.findall( "Iteration_hits/Hit/" ): subject = hit.findtext( "Hit_id" ) + if re.search( '^gi', subject ): + subject = subject.split('|')[1] sLen = hit.findtext( "Hit_len" ) # for every <Hsp> within <Hit> for hsp in hit.findall( "Hit_hsps/Hsp" ):