Script for counting AA triplet occurence in a fasta file.

count_aa_triplet.py

#!/usr/bin/env python

import random

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC

# function to generate random protein sequence
def random_prot(length):
    seq = ''
    for i in xrange(length):
        seq += random.choice(IUPAC.protein.letters)
    return seq

# function to generate list of SeqRecord objects
def seqrecord_gen(num, length):
    seqs = []
    for i in xrange(num):
        seqs.append(SeqRecord(Seq(random_prot(length)),
                    id='fasta'+str(i+1),
                    name='',
                    description=''))
    SeqIO.write(seqs, 'random_proteins.fa', 'fasta')

# function to read fasta file and count triplets
def count_triplet(source):
    triplets = {}
    seqs = SeqIO.parse(source, 'fasta')

    for rec in seqs:
        step = 0
        while step + 3 <= len(rec.seq.tostring()):
            tri = rec.seq.tostring()[0+step:3+step]
            if tri not in triplets:
                triplets[tri] = 1
            else:
                triplets[tri] += 1
            step += 1

    with open('results', 'w') as output:
        for key in sorted(triplets, key=triplets.get, reverse=True):
            output.writelines("{0}: {1}\n".format(key, triplets[key]))

# generate mock file
seqrecord_gen(100, 30)
# count the triplets
count_triplet('random_proteins.fa')