Source code for padmet_utils.connection.gbk_to_faa

# -*- coding: utf-8 -*-
    convert GBK to FAA with Bio package

    usage:    --gbk=FILE --output=FILE [--qualifier=STR] [-v]
        -h --help    Show help.
        --gbk=FILE    path to the gbk file.
        --output=FILE    path to the output, a FAA file.
        --qualifier=STR    the qualifier of the gene id [default: locus_tag].
        -v   print info
import docopt

from padmet.utils.connection import gbk_to_faa

[docs]def main(): args = docopt.docopt(__doc__) gbk_file = args["--gbk"] output = args["--output"] qualifier = args["--qualifier"] verbose = args["-v"] gbk_to_faa.gbk_to_faa(gbk_file, output, qualifier, verbose)
if __name__ == "__main__": main()