def generateRandomGene(seqFileName, newSeqLength):
f = open(seqFileName, 'r')
characterList = []
for line in f:
if line[0] != '>':
characterList += list(line.rstrip('\n'))
homopolCounts = hompol.getCounts(characterList)[1:]
n = len(homopolCounts) - 1
b = bbinom(*bbinom.fit(homopolCounts))
randseq = randgene(hompol.roundTo(newSeqLength, 3), b.ppf)
return randseq
#!/usr/bin/env python3.2
from Bio.Seq import translate
from BioExt import untranslate, randgene
from BioExt.stats import bbinom
from scipy.stats import rv_discrete
samples = [5073, 1337, 380, 131, 36, 20, 1]
n = len(samples) - 1
b = bbinom(*bbinom.fit(samples))
custom = rv_discrete(name='precompbbinom', values=(list(range(n+1)),
[b.pmf(i) for i in range(n+1)]))
# some multiple of 3 to keep frame
randseq = randgene(9999, custom.ppf)
randseqperm = untranslate(translate(randseq))
print(randseq)
