A program for counting dinucleotide frequency for each contig in a .FASTA file

dnf.py

#!/usr/bin/python

import sys
from Bio import SeqIO
from itertools import groupby, product

def canonical(x):
    rules = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
    paired = ''.join(map(lambda x: rules[x], list(x[::-1])))
    return paired if paired < x else x

def dnf(x):
    symbols = sorted(list(set(map(canonical, [''.join(i) for i in product('ACGT',repeat=2)]))))
    splitted = [canonical(x[i:i+2]) for i in range(0, len(x) - 1)]
    counts = [(i, len(list(c))) for i, c in groupby(sorted(splitted))]
    count_dict = dict((x, y) for x, y in counts)
    return map(lambda x: count_dict[x] if x in count_dict else 0, symbols)

with open(sys.argv[2], 'w') as output:
    for seq_record in SeqIO.parse(sys.argv[1], "fasta"):
        result = reduce(lambda x, y: str(x) + '\t' + str(y), dnf(str(seq_record.seq))) + '\n'
        output.write(result)