I want to Blast my data base of sequence (Aminoacid) with a data base. And get sequences which have a given score and e value less than 0.5 . So I ran blast with e-value 0.5 and now i want to isolate those sequences which have scores higher than given value . So i parse it using NCBIXML parser from Biopython. So far i have -
from Bio.Blast import NCBIXML blast = NCBIXML.parse(open(raw_input("Blast file location :"),"rU")) for record in blast : if record.alignments: if record.alignments.hsps.score >= 1000: print record.alignments.hsps.query
This gives me all the sequence but i want it with there respective gene id in seq format so i can use it for further purpose .