concateAlign

#!/usr/bin/pypy

import sys
from Bio import SeqIO
from Bio.Alphabet import DNAAlphabet
import random

if len(sys.argv) < 2:
    print 'USAGE: ./concatenateAlign ALIGN_FASTA [...]'
    sys.exit(1)

files = sys.argv[1:]

d = {}

random.shuffle(files)

for f in files:
    print f
    for s in SeqIO.parse(f, 'fasta'):
        if s.id not in d:
            d[s.id] = s
        else:
            d[s.id] += s

for s in d.itervalues():
    s.seq.alphabet = DNAAlphabet()

SeqIO.write(d.values(), 'ALIGNMENT.nex', 'nexus')