Converts a maf alignment file into fasta file.

maf2fasta.py

#!/usr/bin/env python
"""
Created by Tabea Kischka at 2015-01-27 10:34:05

converts a last maf alignment into a fasta alignment
"""
import sys

path_to_alignio = '/home/tabeah/Scripts/alignio-maf'

try:
    sys.path.insert(1, path_to_alignio)
    from Bio.AlignIO import MafIO
except  ImportError:
    print("ERROR: Couldn't import module MafIO from path '%s'" % \
          (path_to_alignio))
    sys.exit(1)


filnam = sys.argv[1]
fh = open(filnam, 'r')

alignments=[]

for seqobj in MafIO.MafIterator(fh):
        alignments.append(seqobj)



for aln in alignments:

        for record in aln._records:
                sys.stdout.write('>%s\n%s\n'%(record.id, record.seq))