From 06fa848b90982ddcd4308bb88d70a0d5f11f785b Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Tue, 25 Mar 2014 16:33:36 -0400 Subject: add average binding filter --- src/below_melting_temperature.py | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 src/below_melting_temperature.py (limited to 'src/below_melting_temperature.py') diff --git a/src/below_melting_temperature.py b/src/below_melting_temperature.py deleted file mode 100644 index e91e777..0000000 --- a/src/below_melting_temperature.py +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env python -import sys -from Bio.SeqUtils.MeltingTemp import Tm_staluc - -# naiive -def in_temp_range(kmer): - - A = kmer.count('A') - C = kmer.count('C') - G = kmer.count('G') - T = kmer.count('T') - - melt_temp = 0.0; - - if len(kmer) < 13: - melt_temp = ((A+T) * 2) + ((C+G) * 4) - else: - melt_temp = 64.9 + 41*(G+C-16.4)/(A+T+G+C) - - return min_melting_temp < melt_temp < max_melting_temp - -min_melting_temp = float(sys.argv[1]) -max_melting_temp = float(sys.argv[2]) - - -output = [] -for line in sys.stdin: - if min_melting_temp < Tm_staluc(line.split("\t")[0]) < max_melting_temp: - sys.stdout.write(line) -- cgit v1.2.3