fancy consensus builder

cons.py

#!/usr/bin/env python
#http://rosalind.info/problems/cons/

import fastaparse

letters = ["A","C","G","T"]

sequences = [i.seq for i in fastaparse.sequences("temp2")]

#create empty profile matrix
profile = [dict(zip(letters,[0 for col in range(0,4)])) for row in range(0,len(sequences[0]))]

for col,_ in enumerate(sequences[0]):
	for i,_ in enumerate(sequences):
		base = sequences[i][col]
		profile[col][base] += 1

consensus = "".join([max(col,key=col.get) for col in profile])

fastaparse.py

#!/usr/bin/env python
from collections import namedtuple

def sequences(fasta_file):
  seq_buffer = []
	header = ""
	Sequence = namedtuple("Sequence",["header","seq"])

	for line in open(fasta_file):
		line = line.strip()
		if line.startswith(">"):
			if seq_buffer:
				yield Sequence(header,"".join(seq_buffer))
				seq_buffer = []
			header = line;
		else:
			seq_buffer.append(line)
	yield Sequence(header,"".join(seq_buffer))