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#!/usr/bin/env python
# Copyright (c) 2008, Michigan State University.
# Copyright (c) 2016, The Regents of the University of California.
from __future__ import print_function
import argparse
import os
import sys
from screed import ToFasta
# Shell interface to the ToFasta screed conversion function
def main(args):
parser = argparse.ArgumentParser(
description="Convert a screed database to a FASTA file")
parser.add_argument('dbfile')
parser.add_argument('outputfile', default='/dev/stdout', nargs='?')
args = parser.parse_args(args)
if not os.path.isfile(args.dbfile):
print("No such file: %s" % args.dbfile)
exit(1)
n = ToFasta(args.dbfile, args.outputfile)
sys.stderr.write('Wrote {} records in FASTA format.\n'.format(n))
if __name__ == '__main__':
main(sys.argv[1])
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