def writeBothToFile(seqFileName, newSeqLength, randFileName, transFileName): randOutFile = open(randFileName, "w") randOutFile.write("> Randomly generated gene of length %d \n" % int(newSeqLength)) transOutFile = open(transFileName, "w") transOutFile.write("> AA translation and untranslation of randomly generated gene of length %d\n" % int(newSeqLength)) sequence = generateRandomGene(seqFileName, newSeqLength) randOutFile.write(sequence) seqPerm = untranslate(translate(sequence)) transOutFile.write(seqPerm) randOutFile.close() transOutFile.close()
#!/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)