Mercurial > repos > peterjc > blastxml_to_top_descr
comparison 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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8:a8ef75aab1f9 | 9:6aafa0ced802 |
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1 #!/usr/bin/env python | |
2 """Convert a BLAST XML file to a top hits description table. | |
3 | |
4 Takes three command line options, input BLAST XML filename, output tabular | |
5 BLAST filename, number of hits to collect the descriptions of. | |
6 """ | |
7 import sys | |
8 import re | |
9 | |
10 if "-v" in sys.argv or "--version" in sys.argv: | |
11 print "v0.0.5" | |
12 sys.exit(0) | |
13 | |
14 if sys.version_info[:2] >= ( 2, 5 ): | |
15 import xml.etree.cElementTree as ElementTree | |
16 else: | |
17 from galaxy import eggs | |
18 import pkg_resources; pkg_resources.require( "elementtree" ) | |
19 from elementtree import ElementTree | |
20 | |
21 def stop_err( msg ): | |
22 sys.stderr.write("%s\n" % msg) | |
23 sys.exit(1) | |
24 | |
25 #Parse Command Line | |
26 try: | |
27 in_file, out_file, topN = sys.argv[1:] | |
28 except: | |
29 stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, number of hits") | |
30 | |
31 | |
32 try: | |
33 topN = int(topN) | |
34 except ValueError: | |
35 stop_err("Number of hits argument should be an integer (at least 1)") | |
36 if topN < 1: | |
37 stop_err("Number of hits argument should be an integer (at least 1)") | |
38 | |
39 # get an iterable | |
40 try: | |
41 context = ElementTree.iterparse(in_file, events=("start", "end")) | |
42 except: | |
43 stop_err("Invalid data format.") | |
44 # turn it into an iterator | |
45 context = iter(context) | |
46 # get the root element | |
47 try: | |
48 event, root = context.next() | |
49 except: | |
50 stop_err( "Invalid data format." ) | |
51 | |
52 | |
53 re_default_query_id = re.compile("^Query_\d+$") | |
54 assert re_default_query_id.match("Query_101") | |
55 assert not re_default_query_id.match("Query_101a") | |
56 assert not re_default_query_id.match("MyQuery_101") | |
57 re_default_subject_id = re.compile("^Subject_\d+$") | |
58 assert re_default_subject_id.match("Subject_1") | |
59 assert not re_default_subject_id.match("Subject_") | |
60 assert not re_default_subject_id.match("Subject_12a") | |
61 assert not re_default_subject_id.match("TheSubject_1") | |
62 | |
63 | |
64 count = 0 | |
65 pos_count = 0 | |
66 outfile = open(out_file, 'w') | |
67 outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN))) | |
68 for event, elem in context: | |
69 # for every <Iteration> tag | |
70 if event == "end" and elem.tag == "Iteration": | |
71 #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA | |
72 # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> | |
73 # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> | |
74 # <Iteration_query-len>406</Iteration_query-len> | |
75 # <Iteration_hits></Iteration_hits> | |
76 # | |
77 #Or, from BLAST 2.2.24+ run online | |
78 # <Iteration_query-ID>Query_1</Iteration_query-ID> | |
79 # <Iteration_query-def>Sample</Iteration_query-def> | |
80 # <Iteration_query-len>516</Iteration_query-len> | |
81 # <Iteration_hits>... | |
82 qseqid = elem.findtext("Iteration_query-ID") | |
83 if qseqid is None: | |
84 stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)") | |
85 if re_default_query_id.match(qseqid): | |
86 #Place holder ID, take the first word of the query definition | |
87 qseqid = elem.findtext("Iteration_query-def").split(None,1)[0] | |
88 # for every <Hit> within <Iteration> | |
89 hit_descrs = [] | |
90 for hit in elem.findall("Iteration_hits/Hit"): | |
91 #Expecting either this, | |
92 # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> | |
93 # <Hit_def>RecName: Full=Rhodopsin</Hit_def> | |
94 # <Hit_accession>P56514</Hit_accession> | |
95 #or, | |
96 # <Hit_id>Subject_1</Hit_id> | |
97 # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def> | |
98 # <Hit_accession>Subject_1</Hit_accession> | |
99 # | |
100 #apparently depending on the parse_deflines switch | |
101 sseqid = hit.findtext("Hit_id").split(None,1)[0] | |
102 hit_def = sseqid + " " + hit.findtext("Hit_def") | |
103 if re_default_subject_id.match(sseqid) \ | |
104 and sseqid == hit.findtext("Hit_accession"): | |
105 #Place holder ID, take the first word of the subject definition | |
106 hit_def = hit.findtext("Hit_def") | |
107 sseqid = hit_def.split(None,1)[0] | |
108 assert hit_def not in hit_descrs | |
109 hit_descrs.append(hit_def) | |
110 #print "%r has %i hits" % (qseqid, len(hit_descrs)) | |
111 if hit_descrs: | |
112 pos_count += 1 | |
113 hit_descrs = hit_descrs[:topN] | |
114 while len(hit_descrs) < topN: | |
115 hit_descrs.append("") | |
116 outfile.write("%s\t%s\n" % (qseqid, "\t".join(hit_descrs))) | |
117 count += 1 | |
118 # prevents ElementTree from growing large datastructure | |
119 root.clear() | |
120 elem.clear() | |
121 outfile.close() | |
122 print "Of %i queries, %i had BLAST results" % (count, pos_count) |