for cur_record in SeqIO.parse(handle, "fasta"):
codon_position = 0
codon_freq_sequence = str(cur_record.seq).strip().split("@")
for codon_freq in codon_freq_sequence:
if codon_freq != "":
codon = CODON_LABELS[codon_position]
if codon in self.codon_count:
self.codon_count[codon] += int(codon_freq)
else:
pass #raise TypeError("illegal codon %s in gene: %s" % (codon, cur_record.id))
codon_position += 1
#Add this method to CAI class
CAI._count_codons2 = MethodType(_count_codons2, CAI)
CAI._count_codons3 = MethodType(_count_codons3, CAI)
def header_matrix_rcsu(self):
tmp_header = []
tmp_header.append("Name")
for aa in SynonymousCodons:
codons = SynonymousCodons[aa]
for codon in codons:
#first create header for all codons
tmp_header.append(codon)
print '\t'.join(tmp_header)
def generate_matrix_rcsu(self, fasta_file):
"""
