Python program to find the indexes of Cys in the given mutlifasta sequences

Question

[devhimd]

# Program to find the indexes of Cys in the given mutlifasta sequences
    fasta = open('out.fa', 'r+')
    for line in fasta.read().split('\n'):
        if line.startswith(">"):
        header = line
        print(header)
        else: 
            indexes = []
            for i in range(0, len(line)-1):
                 if line[i] == 'C':
                    indexes.append(i+1)
                    print("Cys : ", indexes)

[Mensur Dlakic]

Is there a question?

Answer 1

[Mensur Dlakic]

You will need BioPython for this to work.

import sys
from Bio import SeqIO

FastaFile = open(sys.argv[1], 'r')

for seqs in SeqIO.parse(FastaFile, 'fasta'):
    indexes = []
    name = seqs.id
    seq = seqs.seq
    seqLen = len(seqs)
    for z in range(seqLen):
        if seq[z]=='c' or seq[z]=='C':
            indexes.append(z+1)
    print('>%s' % name)
    print(indexes)

Save as Cys_index.py and run:

python Cys_index.py out.fa