Quick routine for parsing hits out of a blast file using BioPython.

parse_blast_hits.py

import sys
from Bio import SearchIO

# usage: parse_blast_hits.py inputfile > outputfile

file = sys.argv[1]

for qresult in SearchIO.parse(file, 'blast-text'):
  print("%s" % (qresult.id))

setup

# First install BioPython.
# If the following doesn't work (ie, you don't have pip installed),
# then any of the other methods at http://biopython.org/wiki/Download
# should work just as well.

pip install biopython