csv_amino acid composition_columnwise

Question

Sample file:

Column 10: A|Y|E|A
Column 11: W|I|Q|Q

How do I calculate amino acid composition (percentage) specific to each column? for ex: composition of A in column 10 is 50%, E is 25% and Y is 25%.

Biopython provides modules to calculate amino acid composition of entire file in fasta format

from Bio import SeqIO
from Bio.SeqUtils.ProtParam import ProteinAnalysis

for record in SeqIO.parse('output_translation3.fasta', 'fasta'):
    X = ProteinAnalysis(str(record.seq))
    print('\n Results for record: {}'.format(record.id))
    print(X.count_amino_acids()['G'])
    print(X.count_amino_acids()['A'])
    print(X.count_amino_acids()['L'])
    print(X.count_amino_acids()['M'])

Answer 1

from collections import Counter
import re

with open("input.txt") as f:
    for line in f:
        line=line.strip()
        [col,sep,seq] = re.split(r'(: )', line)
        aa = re.split(r'[|]', seq)
        aa_counts = Counter(aa)
        aa_length=len(aa)
        print(col)
        for k,v in aa_counts.items():
            print("  ", k, v/aa_length)

Gives:

Column 10
   A 0.5
   Y 0.25
   E 0.25
Column 11
   W 0.25
   I 0.25
   Q 0.5