Hello everyone,
I am a novice in Python and I have been trying to compute the number of A's occurring in 3rd codon position in a multifasta file. I have written the following code but it does not work.
input_file = open('MG1655.FAS', 'r')
output_file = open('A3_counts.tsv','w')
output_file.write('GenetA3n')
from Bio import SeqIO
for cur_record in SeqIO.parse(input_file, "fasta") :
A3count = 0
gene_name = cur_record.name
sequence = cur_record.seq
for i in range(0, len(sequence), 3):
if sequence[i:i+3]=='a':
A3count = A3count+1
output = '%st%it' % (gene_name, A3count)
output_file.write(output)
output_file.close()
input_file.close()
Please help me with this problem.