o-remove-gaps

#!/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.

import sys

import Oligotyping.lib.fastalib as u


def main(input_fasta_path, output_fasta_path=None, reverse=False):
    if not output_fasta_path:
        output_fasta_path = input_fasta_path + '-GAPS-REMOVED'

    fasta = u.SequenceSource(input_fasta_path)
    output = u.FastaOutput(output_fasta_path)

    while next(fasta):
        if fasta.pos % 1000 == 0:
            sys.stderr.write('\rreads processed so far: %d' % (fasta.pos))
            sys.stderr.flush()
    
        output.write_id(fasta.id)
        output.write_seq(fasta.seq.replace('-', ''), split = False)
        
    fasta.close()
    sys.stderr.write('\n')


if __name__ == '__main__':
    import argparse

    parser = argparse.ArgumentParser(description='Pad sequences with gaps to eliminate length variation')
    parser.add_argument('fasta', metavar = 'FASTA_FILE_PATH',
                        help = 'FASTA file that contains reads to be padded')
    parser.add_argument('-o', '--output', metavar = 'FILE_FILE_PATH', default = None,
                        help = 'Path for output.')


    args = parser.parse_args()

    sys.exit(main(args.fasta,
                  args.output))