running-blast-from-python.md

layout	element	title	language
page	notes	Running BLAST	Python

Import the modules for interfacing with BLAST and parsing the output

from Bio.Blast import NCBIWWW, NCBIXML  

Blast the sequence of interest (in this case using the accession

number result_handle = NCBIWWW.qblast("blastn", "nr", "8332116")  

Parse the resulting output

blast_record = NCBIXML.read(result_handle)  

Loop over the alignments printing some output of interest

E_VALUE_THRESH = 0.004 for alignment in blast_record.alignments:     for hsp in alignment.hsps:         if hsp.expect < E_VALUE_THRESH:             print             print 'Alignment'             print 'sequence:', alignment.title             print 'length:', alignment.length             print 'e value:', hsp.expect             print hsp.query[0:75] + '...'             print hsp.match[0:75] + '...'             print hsp.sbjct[0:75] + '...'