benchmark

Bioinformatics scripts

k8 version 0.2.1: http://sourceforge.net/projects/lh3/files/k8/k8-0.2.1.tar.bz2/download
g++ -o best_hsp best_hsp.c kstring.c -lz

1. blast best hsp parser
   time python best_hsp.py example_blast6out_2000.tsv 1e-5 60 >python.res.tsv
   time k8 best_hsp.js example_blast6out_2000.tsv 1e-5 60 >js.res.tsv
   time python best_hsp.py example_blast6out_2000.tsv 1e-5 60 >python.res.tsv
   time ./best_hsp example_blast6out.tsv 1e-5 60 >c.res.tsv