Mercurial > repos > peterjc > blastxml_to_top_descr
diff blastxml_to_top_descr/blastxml_to_top_descr.py @ 9:6aafa0ced802 draft
Uploaded v0.0.8, moved development to GitHub; no functional changes
author | peterjc |
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date | Tue, 30 Jul 2013 08:07:28 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blastxml_to_top_descr/blastxml_to_top_descr.py Tue Jul 30 08:07:28 2013 -0400 @@ -0,0 +1,122 @@ +#!/usr/bin/env python +"""Convert a BLAST XML file to a top hits description table. + +Takes three command line options, input BLAST XML filename, output tabular +BLAST filename, number of hits to collect the descriptions of. +""" +import sys +import re + +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.5" + sys.exit(0) + +if sys.version_info[:2] >= ( 2, 5 ): + import xml.etree.cElementTree as ElementTree +else: + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree + +def stop_err( msg ): + sys.stderr.write("%s\n" % msg) + sys.exit(1) + +#Parse Command Line +try: + in_file, out_file, topN = sys.argv[1:] +except: + stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, number of hits") + + +try: + topN = int(topN) +except ValueError: + stop_err("Number of hits argument should be an integer (at least 1)") +if topN < 1: + stop_err("Number of hits argument should be an integer (at least 1)") + +# get an iterable +try: + context = ElementTree.iterparse(in_file, events=("start", "end")) +except: + stop_err("Invalid data format.") +# turn it into an iterator +context = iter(context) +# get the root element +try: + event, root = context.next() +except: + stop_err( "Invalid data format." ) + + +re_default_query_id = re.compile("^Query_\d+$") +assert re_default_query_id.match("Query_101") +assert not re_default_query_id.match("Query_101a") +assert not re_default_query_id.match("MyQuery_101") +re_default_subject_id = re.compile("^Subject_\d+$") +assert re_default_subject_id.match("Subject_1") +assert not re_default_subject_id.match("Subject_") +assert not re_default_subject_id.match("Subject_12a") +assert not re_default_subject_id.match("TheSubject_1") + + +count = 0 +pos_count = 0 +outfile = open(out_file, 'w') +outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN))) +for event, elem in context: + # for every <Iteration> tag + if event == "end" and elem.tag == "Iteration": + #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA + # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + # <Iteration_query-len>406</Iteration_query-len> + # <Iteration_hits></Iteration_hits> + # + #Or, from BLAST 2.2.24+ run online + # <Iteration_query-ID>Query_1</Iteration_query-ID> + # <Iteration_query-def>Sample</Iteration_query-def> + # <Iteration_query-len>516</Iteration_query-len> + # <Iteration_hits>... + qseqid = elem.findtext("Iteration_query-ID") + if qseqid is None: + stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)") + if re_default_query_id.match(qseqid): + #Place holder ID, take the first word of the query definition + qseqid = elem.findtext("Iteration_query-def").split(None,1)[0] + # for every <Hit> within <Iteration> + hit_descrs = [] + for hit in elem.findall("Iteration_hits/Hit"): + #Expecting either this, + # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> + # <Hit_def>RecName: Full=Rhodopsin</Hit_def> + # <Hit_accession>P56514</Hit_accession> + #or, + # <Hit_id>Subject_1</Hit_id> + # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def> + # <Hit_accession>Subject_1</Hit_accession> + # + #apparently depending on the parse_deflines switch + sseqid = hit.findtext("Hit_id").split(None,1)[0] + hit_def = sseqid + " " + hit.findtext("Hit_def") + if re_default_subject_id.match(sseqid) \ + and sseqid == hit.findtext("Hit_accession"): + #Place holder ID, take the first word of the subject definition + hit_def = hit.findtext("Hit_def") + sseqid = hit_def.split(None,1)[0] + assert hit_def not in hit_descrs + hit_descrs.append(hit_def) + #print "%r has %i hits" % (qseqid, len(hit_descrs)) + if hit_descrs: + pos_count += 1 + hit_descrs = hit_descrs[:topN] + while len(hit_descrs) < topN: + hit_descrs.append("") + outfile.write("%s\t%s\n" % (qseqid, "\t".join(hit_descrs))) + count += 1 + # prevents ElementTree from growing large datastructure + root.clear() + elem.clear() +outfile.close() +print "Of %i queries, %i had BLAST results" % (count, pos_count)