# calculate the RSCU value for each of the codons
for codon in codons:
denominator = float(float(1) / float(len(codons))) * float(total)
#denominator = float(total) / len(codons)
if self.codon_count[codon] > 0:
RCSU_vector.append(self.codon_count[codon] / denominator)
else:
#TODO: give some kine of warning message that codon count is 0
RCSU_vector.append(0)
# print aa, "@", codons, "@",len(codons), "@",total, "@",rcsu
print os.path.splitext(os.path.basename(fasta_file))[0] + '\t' + '\t'.join(
['{:.6f}'.format(x) for x in RCSU_vector])
#Add these methods to CAI class
CAI.generate_matrix_rcsu = MethodType(generate_matrix_rcsu, CAI)
CAI.cutg_generate_matrix_rcsu = MethodType(cutg_generate_matrix_rcsu, CAI)
CAI.header_matrix_rcsu = MethodType(header_matrix_rcsu, CAI)
# define function that dowloads GenBank files and extracts CDS/gene sequences
def extract_gb_ORFs(gi_id):
"""
Extract feature sequences from genbak file
"""
handle = Entrez.efetch(db="nuccore",
id=gi_id,
rettype="gb",
retmode="text")
#record = SeqIO.parse(handle, "gb")
