[BioPython] Running Blast locally

[Muthuraman, Manickam]

Dear Christof

Your command also works  separately but my question was how to intergrate blast in biopython script.

in biopython tutorial and cookbook they have the follwoing code where i need to provide the path to database ,file to blast and blast_exe.

I am not clear how to set the path for seq_file,db and exe.

import os
my_blast_db=os.path.join(os.getcwd(),'at-est','a-cds-10-7.fasta')
my_blast_file=os.path.join(os.getcwd(),'at-est','test_blast','sorghum_est-test.fasta')
my_blast_exe=os.path.join(os.getcwd(),'blast','/home/manickam/blast/blastall')


here is the whole script
import os
my_blast_db=os.path.join(os.getcwd(),'at-est','a-cds-10-7.fasta')
my_blast_file=os.path.join(os.getcwd(),'at-est','test_blast','sorghum_est-test.fasta')
my_blast_exe=os.path.join(os.getcwd(),'blast','/home/manickam/blast/blastall')
from Bio.Blast import NCBIStandalone
blast_out,error_info=NCBIStandalone.blastall(my_blast_exe,'blastp',my_blast_db,my_blast_file)
b_parser=NCBIStandalone.BlastParser()
b_iterator=NCBIStandalone.Iterator(blast_out,b_parser)
b_record=b_iterator.next()
while 1:
    b_record=b_iterator.next()
    if b_record is None:
        break
    for alignment in b_record.alignments:
        print "inside 2 loop"
        for hsp in alignment.hsps:
            print "inside 1 loop"
            print 'seq:',alignment.title

it runs but b_record is None so it comes out of the while loop at first time itself. so it mean i am not getting out put of the blast.

from
manickam