Mercurial > repos > devteam > megablast_xml_parser

comparison megablast_xml_parser.py @ 0:35ff246876fc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imported from capsule None
author devteam
date Mon, 19 May 2014 10:59:33 -0400
parents
children 3ce5d56297ed
comparison
equal deleted inserted replaced
-1:000000000000 0:35ff246876fc
1 #!/usr/bin/env python
2
3 import sys, os, re
4
5 if sys.version_info[:2] >= ( 2, 5 ):
6 import xml.etree.cElementTree as ElementTree
7 else:
8 from galaxy import eggs
9 import pkg_resources; pkg_resources.require( "elementtree" )
10 from elementtree import ElementTree
11
12 def stop_err( msg ):
13 sys.stderr.write( "%s\n" % msg )
14 sys.exit()
15
16 def __main__():
17 source = sys.argv[1]
18 hspTags = [
19 "Hsp_bit-score",
20 "Hsp_evalue",
21 "Hsp_query-from",
22 "Hsp_query-to",
23 "Hsp_hit-from",
24 "Hsp_hit-to",
25 "Hsp_query-frame",
26 "Hsp_hit-frame",
27 "Hsp_identity",
28 "Hsp_align-len",
29 "Hsp_qseq",
30 "Hsp_hseq",
31 "Hsp_midline"
32 ]
33 hspData = []
34
35 # get an iterable
36 try:
37 context = ElementTree.iterparse( source, events=( "start", "end" ) )
38 except:
39 stop_err( "Invalid data format." )
40 # turn it into an iterator
41 context = iter( context )
42 # get the root element
43 try:
44 event, root = context.next()
45 except:
46 stop_err( "Invalid data format." )
47
48 outfile = open( sys.argv[2], 'w' )
49 try:
50 for event, elem in context:
51 # for every <Iteration> tag
52 if event == "end" and elem.tag == "Iteration":
53 query = elem.findtext( "Iteration_query-def" )
54 qLen = elem.findtext( "Iteration_query-len" )
55 # for every <Hit> within <Iteration>
56 for hit in elem.findall( "Iteration_hits/Hit" ):
57 subject = hit.findtext( "Hit_id" )
58 if re.search( '^gi', subject ):
59 subject = subject.split('|')[1]
60 sLen = hit.findtext( "Hit_len" )
61 # for every <Hsp> within <Hit>
62 for hsp in hit.findall( "Hit_hsps/Hsp" ):
63 outfile.write( "%s\t%s\t%s\t%s" % ( query, qLen, subject, sLen ) )
64 for tag in hspTags:
65 outfile.write("\t%s" %(hsp.findtext( tag )))
66 #hspData.append( hsp.findtext( tag ) )
67 #hspData = []
68 outfile.write('\n')
69 # prevents ElementTree from growing large datastructure
70 root.clear()
71 elem.clear()
72 except:
73 outfile.close()
74 stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] )
75
76 outfile.close()
77
78 if __name__ == "__main__": __main__()