fasta2Nexus

#!/usr/bin/pypy

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

if len(sys.argv) < 2:
    print 'USAGE: ./fasta2Nexus ALIGN_FASTA'
    sys.exit(1)

infile = sys.argv[1]

d = {}

for s in SeqIO.parse(infile, 'fasta'):
    # Fix some nexus and newick format odd things
    if '-' in s.id:
        s.id = s.id.replace('-', 'CHANGETHIS')
    try:
        int(s.id)
        s.id = 'REMOVETHIS%s'%s.id
    except:pass

    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(), '%s.nex'%infile, 'nexus')