Question: A3 count (count of A occurring in 3rd codon position) in multifasta file
6 months ago by
annushreekurmi • 0
annushreekurmi • 0 wrote:
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('Gene\tA3\n') 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 = '%s\t%i\t' % (gene_name, A3count) output_file.write(output) output_file.close() input_file.close()
Please help me with this problem.
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