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jameslz / benchmark

Bioinformatics scripts
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python is the slowest on my computer #1

Open gahoo opened 9 years ago

gahoo commented 9 years ago

on my laptop, js is still the fastest and python is the slowest.

try this one liner awk version:

best_hsp.sh

cat $1|awk -v max_evalue=$2 -v min_bit=$3 '{if( $1 !~ "^#" && init != $1 ){init=$1;evalue=$11;bit=$12;if(evalue < max_evalue && bit > min_bit)print}}'

time sh best_hsp.sh example_blast6out_2000.tsv 1e-5 60 > /dev/null

jameslz commented 9 years ago

if you use large data sets, you get the different result. python is faster than perl.