[BioPython] Need help parsing Blastoutput
Halima Rabiu
halima at mancala.cbio.uct.ac.za
Tue Apr 18 15:06:02 UTC 2006
thanks
please see the attchment a copy of my script and copy of my Blast output
Thanks
On Thu, 13 Apr 2006, Michiel De Hoon wrote:
> Could you send us the script you were using?
>
> --Michiel.
>
> Michiel de Hoon
> Center for Computational Biology and Bioinformatics
> Columbia University
> 1150 St Nicholas Avenue
> New York, NY 10032
>
>
>
> -----Original Message-----
> From: biopython-bounces at lists.open-bio.org on behalf of Halima Rabiu
> Sent: Thu 4/13/2006 11:07 AM
> To: biopython at lists.open-bio.org
> Subject: [BioPython] Need help parsing Blastoutput
>
> Hi All,
> I have a BLAST output from a local blast
> I need to calculate my % alignment coverage as regard to my subject
> I try parsed the blast output and wanted to print the
> sbjct Start and Sbjct end. but I could not is there anyway I could this
> try to get mach coverage between my querry and subject I dont need
> Identities,but total % alignment for querry or subject.
> Thanks
> Halimah
>
> _______________________________________________
> BioPython mailing list - BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>
-------------- next part --------------
#! /usr/local/bin/python2.4
#halimah
#16-04-2006
from string import split
from Bio.Blast import NCBIStandalone
b_out = open('Enterococcus_out','r')
b_parser = NCBIStandalone.BlastParser()
b_iterator = NCBIStandalone.Iterator(b_out,b_parser)
E_VALUE_THRESH = 1.0
while 1:
b_record = b_iterator.next()
print "The following results are for query " + b_record.query
print 'len of query:',b_record.query_letters
if b_record is None:
break
for alignment in b_record.alignments:
for hsp in alignment.hsps:
if hsp.expect <= E_VALUE_THRESH:
print '****Alignment****'
print 'title:', alignment.title
print 'length:', alignment.length
print 'e value:', hsp.expect
print 'subjectstart:',hsp.sbjct_start
print 'subject end:', hsp.sbject_end
More information about the Biopython
mailing list