diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-24 15:36:53 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-24 15:36:53 -0400 |
| commit | 65e9bc6772f4538078d0eb1d78ff7b08df6d9c4e (patch) | |
| tree | 71efc1428139b8b9bc67f45ce79bee9c65b7db24 /src | |
| parent | 375ab82530af1f6dbf26db6222680d483014a0e3 (diff) | |
use biopython's temperature calculator... slow as dirt
Diffstat (limited to 'src')
| -rw-r--r-- | src/below_melting_temperature.py | 7 |
1 files changed, 5 insertions, 2 deletions
diff --git a/src/below_melting_temperature.py b/src/below_melting_temperature.py index e2521db..e91e777 100644 --- a/src/below_melting_temperature.py +++ b/src/below_melting_temperature.py @@ -1,5 +1,8 @@ +#!/usr/bin/env python import sys +from Bio.SeqUtils.MeltingTemp import Tm_staluc +# naiive def in_temp_range(kmer): A = kmer.count('A') @@ -22,5 +25,5 @@ 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 + if min_melting_temp < Tm_staluc(line.split("\t")[0]) < max_melting_temp: + sys.stdout.write(line) |