Mercurial > repos > devteam > megablast_xml_parser

comparison megablast_xml_parser.py @ 1:fbff957a3655 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser commit 3ccddd4e2032535ead030efa401e690ffb80d145"
author devteam
date Wed, 09 Sep 2020 10:27:39 +0000
parents 03ca082aeb2e
children
comparison
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0:03ca082aeb2e 1:fbff957a3655
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2
3 import sys, os, re
4 2
5 if sys.version_info[:2] >= ( 2, 5 ): 3 import re
6 import xml.etree.cElementTree as ElementTree 4 import sys
7 else: 5 import xml.etree.cElementTree as ElementTree
8 from galaxy import eggs
9 import pkg_resources; pkg_resources.require( "elementtree" )
10 from elementtree import ElementTree
11 6
12 def stop_err( msg ):
13 sys.stderr.write( "%s\n" % msg )
14 sys.exit()
15 7
16 def __main__(): 8 def __main__():
17 source = sys.argv[1] 9 source = sys.argv[1]
18 hspTags = [ 10 hspTags = ["Hsp_bit-score",
19 "Hsp_bit-score", 11 "Hsp_evalue",
20 "Hsp_evalue", 12 "Hsp_query-from",
21 "Hsp_query-from", 13 "Hsp_query-to",
22 "Hsp_query-to", 14 "Hsp_hit-from",
23 "Hsp_hit-from", 15 "Hsp_hit-to",
24 "Hsp_hit-to", 16 "Hsp_query-frame",
25 "Hsp_query-frame", 17 "Hsp_hit-frame",
26 "Hsp_hit-frame", 18 "Hsp_identity",
27 "Hsp_identity", 19 "Hsp_align-len",
28 "Hsp_align-len", 20 "Hsp_qseq",
29 "Hsp_qseq", 21 "Hsp_hseq",
30 "Hsp_hseq", 22 "Hsp_midline"]
31 "Hsp_midline"
32 ]
33 hspData = []
34 23
35 # get an iterable 24 # get an iterable
36 try: 25 try:
37 context = ElementTree.iterparse( source, events=( "start", "end" ) ) 26 context = ElementTree.iterparse(source, events=("start", "end"))
38 except: 27 except Exception:
39 stop_err( "Invalid data format." ) 28 sys.exit("Invalid data format.")
40 # turn it into an iterator 29 # turn it into an iterator
41 context = iter( context ) 30 context = iter(context)
42 # get the root element 31 # get the root element
43 try: 32 try:
44 event, root = context.next() 33 event, root = next(context)
45 except: 34 except Exception:
46 stop_err( "Invalid data format." ) 35 sys.exit("Invalid data format.")
47 36
48 outfile = open( sys.argv[2], 'w' ) 37 with open(sys.argv[2], 'w') as outfile:
49 try: 38 try:
50 for event, elem in context: 39 for event, elem in context:
51 # for every <Iteration> tag 40 # for every <Iteration> tag
52 if event == "end" and elem.tag == "Iteration": 41 if event == "end" and elem.tag == "Iteration":
53 query = elem.findtext( "Iteration_query-def" ) 42 query = elem.findtext("Iteration_query-def")
54 qLen = elem.findtext( "Iteration_query-len" ) 43 qLen = elem.findtext("Iteration_query-len")
55 # for every <Hit> within <Iteration> 44 # for every <Hit> within <Iteration>
56 for hit in elem.findall( "Iteration_hits/Hit" ): 45 for hit in elem.findall("Iteration_hits/Hit"):
57 subject = hit.findtext( "Hit_id" ) 46 subject = hit.findtext("Hit_id")
58 if re.search( '^gi', subject ): 47 if re.search('^gi', subject):
59 subject = subject.split('|')[1] 48 subject = subject.split('|')[1]
60 sLen = hit.findtext( "Hit_len" ) 49 sLen = hit.findtext("Hit_len")
61 # for every <Hsp> within <Hit> 50 # for every <Hsp> within <Hit>
62 for hsp in hit.findall( "Hit_hsps/Hsp" ): 51 for hsp in hit.findall("Hit_hsps/Hsp"):
63 outfile.write( "%s\t%s\t%s\t%s" % ( query, qLen, subject, sLen ) ) 52 outfile.write("%s\t%s\t%s\t%s" % (query, qLen, subject, sLen))
64 for tag in hspTags: 53 for tag in hspTags:
65 outfile.write("\t%s" %(hsp.findtext( tag ))) 54 outfile.write("\t%s" % (hsp.findtext(tag)))
66 #hspData.append( hsp.findtext( tag ) ) 55 outfile.write('\n')
67 #hspData = [] 56 # prevents ElementTree from growing large datastructure
68 outfile.write('\n') 57 root.clear()
69 # prevents ElementTree from growing large datastructure 58 elem.clear()
70 root.clear() 59 except Exception:
71 elem.clear() 60 sys.exit("The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1])
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 61
76 outfile.close()
77 62
78 if __name__ == "__main__": __main__() 63 if __name__ == "__main__":
64 __main__()