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#!/usr/bin/env python2.7
import sys
import os
fg_mers = {}
bg_mers = {}
fg_weight = float(os.environ.get("fg_weight", 0))
max_check = int(os.environ.get("max_check", 0))
if(len(sys.argv) == 3):
fg_count_fn = sys.argv[1]
bg_count_fn = sys.argv[2]
else:
print len(sys.argv)
sys.stderr.write("please specify your inputs\n")
sys.stderr.write("ex: select_mers.py fg_counts bg_count\n")
exit(1)
# select mers based on our 'selectivity' measure. (count in fg) / (count in bg)
def select_mers(fg_mers, bg_mers):
# populate our bg_arr and fg_arr as well as our mer arr.
score = {}
for mer in fg_mers.keys():
score[mer] = (fg_mers[mer] / bg_mers[mer]) * (fg_mers[mer]**fg_weight)
sorted_scored_mers = sorted(score, key=score.get)
for mer in sorted_scored_mers:
print mer, int(fg_mers[mer]), int(bg_mers[mer]), (fg_mers[mer] / bg_mers[mer]) * (fg_mers[mer]**fg_weight)
def main():
fg_count_fh = open(fg_count_fn, "r")
bg_count_fh = open(bg_count_fn, "r")
# copy in our fg_mers and counts
for mers,fh in [(fg_mers, fg_count_fh), (bg_mers, bg_count_fh)]:
for line in fh:
(mer, count) = line.split()
mers[mer] = float(count)
for mer in fg_mers.keys():
if mer not in bg_mers:
bg_mers[mer] = 1
for mer in bg_mers.keys():
if mer not in fg_mers:
del bg_mers[mer]
selected = select_mers(fg_mers, bg_mers)
if __name__ == "__main__":
sys.exit(main())
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