[BioPython] parsing the blastoutput and printing the alingment

[Michiel Jan Laurens de Hoon]

Muthuraman, Manickam wrote:
> 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
>     
> Traceback (most recent call last):
>   File "<input>", line 1, in ?
> AttributeError: Iterator instance has no attribute 'alignments'
> 
Use:
b_record = b_iterator1.next()
for alignment in b_record.alignments:
    ...

Just like the example in the tutorial.

--Michiel.


-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032