extract-screed.py

#! /usr/bin/env python
"""
Usage:

python -m screed db <sequencefile>
python extract-screed.py <list of names> <sequencefile>
"""
import argparse, screed, sys

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('names')
    parser.add_argument('dbfile')
    args = parser.parse_args()

    names = set([ x.strip() for x in open(args.names) ])
    found = set()

    db = screed.ScreedDB(args.dbfile)

    for name in names:
        record = db.get(name)
        if record:
            print('>{}\n{}'.format(record.name, record.sequence))
        else:
            sys.stderr.write('key "{}" not in database\n'.format(name))


if __name__ == '__main__':
    main()