From 5df2b9950b1748148b90c33b7a004056491f9e51 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 17 Jan 2014 14:32:06 -0500 Subject: move melting temp py script to src --- src/below_melting_temperature.py | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 src/below_melting_temperature.py (limited to 'src') diff --git a/src/below_melting_temperature.py b/src/below_melting_temperature.py new file mode 100644 index 0000000..e2521db --- /dev/null +++ b/src/below_melting_temperature.py @@ -0,0 +1,26 @@ +import sys + +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 in_temp_range(line.split("\t")[0]): + sys.stdout.write(line) \ No newline at end of file -- cgit v1.2.3