o-gen-dicts-for-qual-stats

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

# Copyright (C) 2010 - 2012, 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.

# get me some alignments and qual scores:
#
# python $me.py fasta.fa fasta.qual
#

import sys
import pickle

from Oligotyping.utils.utils import get_quals_dict


alignment_file = sys.argv[1]
quals_file = sys.argv[2]

quals_dict = get_quals_dict(quals_file, alignment_file)

pickle.dump(quals_dict, open(alignment_file + '-QUALS-DICT', 'w'))

print('output file:')
print('  - "%s"' % (alignment_file + '-QUALS-DICT'))