Hi,
I am having problem while running NCBIStandalone library of biopython. i want to retrieve sequence titles from output of blast but it gives error on iterator.
Following is the code to retrieve these sequence titles.
result_handle= open("foo.txt")
blast_parser = NCBIStandalone.BlastParser()
blast_iterator = NCBIStandalone.Iterator(result_handle, blast_parser)
print blast_iterator
for blast_record in blast_iterator:
print blast_record
E_VALUE_THRESH = 0.0
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH:
print 'sequence:', alignment.title
But it gives following errors. it makes iterator properly but does not loop it.
<Bio.Blast.NCBIStandalone.Iterator object at 0x1aa6450>
Traceback (most recent call last):
File "blast2.py", line 45, in <module>
for blast_record in blast_iterator:
File "/usr/lib/pymodules/python2.7/Bio/Blast/NCBIStandalone.py", line 1659, in next
return self._parser.parse(File.StringHandle(data))
File "/usr/lib/pymodules/python2.7/Bio/Blast/NCBIStandalone.py", line 818, in parse
self._scanner.feed(handle, self._consumer)
File "/usr/lib/pymodules/python2.7/Bio/Blast/NCBIStandalone.py", line 112, in feed
read_and_call_until(uhandle, consumer.noevent, contains='BLAST')
File "/usr/lib/pymodules/python2.7/Bio/ParserSupport.py", line 337, in read_and_call_until
line = safe_readline(uhandle)
File "/usr/lib/py ...