def importgeneticcodedegeneracy(geneticcode=None): """ """ if not geneticcode: geneticcode = importgeneticcode() degeneracy = {} for triplet, aa in geneticcode.iteritems(): if degeneracy.has_key(aa): degeneracy[aa].append(triplet) else: degeneracy[aa] = [ triplet ] return degeneracy
for triplet in triplets: tripletbiasaward[triplet] = { 0: {}, 1: {}, 2: {} } for frame in [0,1,2]: bases = [ trip[frame] for trip in triplets ] if len(Set(bases)) == 1: # no choice in base for this frame for this AA! pass else: for base in Set(bases): tripletbiasaward[triplet][frame][base] = 1 # and return this dict return tripletbiasaward # end of function importtripletbiasaward GENETICCODE = importgeneticcode() DEGENERACY = importgeneticcodedegeneracy(GENETICCODE) TRIPBIASAWARD = importtripletbiasaward(DEGENERACY) def basebias(seq,GENETICCODE=GENETICCODE,DEGENERACY=DEGENERACY,TRIPBIASAWARD=TRIPBIASAWARD): """ """ biasperframe={ 0: { 'A': 0, 'T': 0, 'G': 0, 'C': 0 }, 1: { 'A': 0, 'T': 0, 'G': 0, 'C': 0 }, 2: { 'A': 0, 'T': 0, 'G': 0, 'C': 0 }, } cnt = 0 for triplet in [ seq[offset:offset+3].upper() for offset in range(0,len(seq),3) ]: try: