[BioPython] Help for BLAST
Sameet Mehta
sameet at nccs.res.in
Tue Jul 27 00:56:00 EDT 2004
Hi,
I want to do a NCBIWWW BLAST, from a set of files that i havve. The
sequences are in FASTA format. The Blast Runs perfectly, however, i have
problems parsing the output. I am doing the following :
>>> from Bio import Fasta
>>> from Bio.Blast import NCBIWWW
>>> file_to_blast = open('C:\Sameet\Data\H9.txt', 'r')
>>> f_iterator = Fasta.Iterator(file_to_blast)
>>> f_record = f_iterator.next()
>>> b_result = NCBIWWW.qblast('blastn', 'nr', f_record, descriptions=20,
alignments=20)
>>> b_parser = NCBIWWW.BlastParser()
>>> b_record = b_parser.parse(b_result)
I am getting the follwing error
Traceback (most recent call last):
File "<pyshell#8>", line 1, in -toplevel-
b_record = b_parser.parse(b_result)
File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 47, in
parse
self._scanner.feed(handle, self._consumer)
File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 101, in
feed
self._scan_rounds(uhandle, consumer)
File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 244, in
_scan_rounds
self._scan_alignments(uhandle, consumer)
File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 327, in
_scan_alignments
self._scan_pairwise_alignments(uhandle, consumer)
File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 350, in
_scan_pairwise_alignments
self._scan_one_pairwise_alignment(uhandle, consumer)
File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 381, in
_scan_one_pairwise_alignment
self._scan_alignment_header(uhandle, consumer)
File "C:\Python23\lib\site-packages\Bio\Blast\NCBIWWW.py", line 419, in
_scan_alignment_header
raise SyntaxError, "I missed the Length in an alignment header"
SyntaxError: I missed the Length in an alignment header
Am i missing something or doing something wrong. I need this information
urgently.
Regards
sameet
--
National Centre for Cell Science, Pune
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