o-generate-consensus-from-alignment

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (C) 2013, A. Murat Eren
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# Please read the COPYING file.

import sys
import os
import operator

import Oligotyping.lib.fastalib as u

consensus_sequence = ''

fasta = u.SequenceSource(sys.argv[1])
next(fasta)
alignment_length = len(fasta.seq)
consensus_dict = {}
for i in range(0, alignment_length):
    consensus_dict[i] = {'A': 0, 'T': 0, 'C': 0, 'G': 0, '-': 0}

fasta.reset()

while next(fasta):
    for pos in range(0, alignment_length):
        consensus_dict[pos][fasta.seq[pos]] += 1

for pos in range(0, alignment_length):
    consensus_sequence += sorted(iter(consensus_dict[pos].items()), key=operator.itemgetter(1), reverse=True)[0][0]

print('>' + os.path.basename(sys.argv[1]))
print(consensus_sequence)