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:
