Quick script to compare SearchIO and NCBIXML blast xml parser performance

blastxml_benchmark.py

#!/usr/bin/env python

# quick script to compare SearchIO and NCBIXML blast xml parser performance


searchio="""
from Bio import SearchIO

for result in SearchIO.parse('%s', 'blast-xml'):
    query_id = result.id

"""

ncbixml="""
from Bio.Blast import NCBIXML

with open('%s', 'r') as xmlfile:
    for result in NCBIXML.parse(xmlfile):
        query_id = result.query_id

"""

import timeit

repeat = 10
xmlfile = 'tblastx_human_wnts.xml'

searchio_time = timeit.timeit(searchio % xmlfile, number=repeat)
ncbixml_time = timeit.timeit(ncbixml % xmlfile, number=repeat)

searchio_avg = searchio_time / float(repeat)
ncbixml_avg = ncbixml_time / float(repeat)

print "Repeats    : %i" % repeat
print "SearchIO   : %.3f (%.3f)" % (searchio_time, searchio_avg)
print "NCBXIML    : %.3f (%.3f)" % (ncbixml_time, ncbixml_avg)
print "Difference : %.3f (%.3f)" % (searchio_time - ncbixml_time, \
        searchio_avg - ncbixml_avg)