diff ngsutils/support/llh.py @ 2:7a68005de299 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author iuc
date Sun, 27 Nov 2016 15:01:21 -0500
parents 4e4e4093d65d
children
line wrap: on
line diff
--- a/ngsutils/support/llh.py	Sun Dec 06 05:03:12 2015 -0500
+++ b/ngsutils/support/llh.py	Sun Nov 27 15:01:21 2016 -0500
@@ -1,14 +1,16 @@
 '''
 Methods for calculating log-likelihoods for nucleotide frequencies
 '''
+import collections
 import math
-import collections
+
 from ngsutils.support import memoize
 
 _default_background = {'A': 0.3, 'T': 0.3, 'C': 0.2, 'G': 0.2}
 
 NucleotideLogLikelihood = collections.namedtuple('NucleotideLogLikelihood', 'A C G T pseudo')
 
+
 @memoize
 def pseudo_count(N, bg):
     '''
@@ -49,7 +51,6 @@
     return NucleotideLogLikelihood(math.log(freqA / bg['A']), math.log(freqC / bg['C']), math.log(freqG / bg['G']), math.log(freqT / bg['T']), pseudo)
 
 
-
 if __name__ == '__main__':
     import doctest
     doctest.testmod()