comparison filter_by_fasta_ids.py @ 7:0a189243186d draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745

6:c67bd5acbae2

            return atarget
    return None


def main():
    ''' the main function'''

    used_sequences = set()
    work_summary = {'wanted': 0, 'found': 0, 'duplicates': 0}
    targets = []

    with open(sys.argv[1]) as f_target:
        for line in f_target.readlines():
            targets.append(">%s" % line.strip().upper())

    work_summary['wanted'] = len(targets)

    for entry in FASTAReader_gen(sys.argv[2]):
        target_matched_results = target_match(targets, entry.header)

7:0a189243186d

            return atarget
    return None


def main():
    used_sequences = set()
    work_summary = {'wanted': 0, 'found': 0, 'duplicates': 0}

    with open(sys.argv[1]) as f_target:
        targets = [">%s" % _.strip().upper() for _ in f_target]

    work_summary['wanted'] = len(targets)

    for entry in FASTAReader_gen(sys.argv[2]):
        target_matched_results = target_match(targets, entry.header)