[BioPython] Error XML Parser and another doubt
Rodrigo faccioli
rodrigo_faccioli at uol.com.br
Tue Jan 27 11:31:41 EST 2009
I have a error about read a XML file which is result from NCBIWWW.qblast.
For this work, I used biopython 1.45 and python 2.5.
The source-code is below:
from Bio.Blast import NCBIXML
import sys
def readxml(filenamexml):
E_VALUE_THRESH = 0.04
result_handle = open(filenamexml)
blast_records = NCBIXML.parse(result_handle)
for alignment in blast_records:
for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH:
print '****Alignment****'
print 'sequence:', alignment.title
print 'length:', alignment.length
print 'e value:', hsp.expect
print hsp.query[0:75] + '...'
print hsp.match[0:75] + '...'
print hsp.sbjct[0:75] + '...'
def main():
filenamexml = sys.argv[1]
readxml(filenamexml)
print "Done"
main()
The error message is:
Traceback (most recent call last):
File "src/readxml.py", line 26, in <module>
main()
File "src/readxml.py", line 23, in main
readxml(filenamexml)
File "src/readxml.py", line 10, in readxml
for alignment in blast_records:
File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 574, in
parse
expat_parser.Parse(text, False)
File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 98, in
endElement
eval("self.%s()" % method)
File "<string>", line 1, in <module>
File "/usr/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 214, in
_end_BlastOutput_version
self._header.date = self._value.split()[2][1:-1]
IndexError: list index out of range
I'm very new in Python and BioPython. Sincerely, this is my first program
without tutorial.
I have another doubt: Is there a way (website, program) that read a xml file
from blast and shows like ncbi web site?
Thanks for any help.
--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
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