[BioPython] Running Blast locally

[Muthuraman, Manickam]

Dear Peter

i am not clear about the subtopic running blast locally

let me explain in detail
i have blast executable files in my home directory i.e
/home/manickam/blast/blastall

i have my database files of nr,swissprot,pdb in /usr/junk/

the files which i can see under /usr/junk/        folder are 
nr.00.phr    
 nr.00.ppi  
nr.01.phr     
nr.01.ppi  nr.pal        
pdbaa.00.msk

lot in there and there extenstions are *.phr , ppi ,pal,msk,psq

i am not clear from the manual where do i need to provide the input sequences and how to i store the out put after running the local blast.

below is the following code which i tried and it works but b_record is none.

mport 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:
        for hsp in alignment.hsps:
            print 'seq:',alignment.title

from
manickam

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