Relative frequencies of the nucleotides in Fasta files

Relative frequencies of the nucleotides in Fasta files

1

I have 2 fasta files (File A, File B) each one contains sequence, How can I report the relative frequencies of the nucleotides in set A and set B with python?

Thanks in advance


fasta

• 558 views

Hi check the link in the comments and read the biopython documentation. Until then, try this:

#!/usr/bin/env python
from Bio import SeqIO
for fasta_path in ['/path/to/fasta1', '/path/to/fasta2']:
    count_nucletides = dict([(i,0) for i in "ACTG"])
    for record in SeqIO.parse(fasta_path, 'fasta'):
        for nucleotide in count_nucletides:
            count_nucletides[nucleotide] += record.seq.count(nucleotide)
    print(fasta_path)
    print('n'.join(['{}: {}'.format(i,count_nucletides[i]) for i in count_nucletides]))


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