[BioPython] parsing the blastoutput and printing the alingment
Peter
biopython at maubp.freeserve.co.uk
Wed Jun 14 21:48:20 UTC 2006
Muthuraman, Manickam wrote:
> I am new to python
>
> I am getting error in parsing blastoutput more over the same problem
> was been addressed by Michiel De Hoon but i could not clear...
>
> blast_out=open('my_blast.out','r')
> from Bio.Blast import NCBIStandalone
> from Bio.Blast import NCBIXML
> b_parser=NCBIXML.BlastParser()
> b_iterator1=NCBIStandalone.Iterator(blast_out,b_parser)
> for alignment in b_iterator1.alignments:
> for hsp in alignment.hsps:
> print 'seq:',alignment.title
>
Your example code is wrong. The iterator object will return blast
record objects (which have an alignments property).
Try something like this:
blast_out=open('my_blast.out','r')
from Bio.Blast import NCBIStandalone
from Bio.Blast import NCBIXML
b_parser=NCBIXML.BlastParser()
b_iterator=NCBIStandalone.Iterator(blast_out,b_parser)
for b_record in b_iterator:
for alignment in b_record.alignments:
for hsp in alignment.hsps:
print 'seq:',alignment.title
Or for a full and tested example, try this :
http://bugzilla.open-bio.org/attachment.cgi?id=293&action=view
Peter
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