Source code for conkit.command_line.conkit_convert

#!/usr/bin/env python
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"""This script provides direct access to ConKit's conversion algorithms.

This script can convert either contact prediction files or sequence files.
In case of the latter, a file with a single or multiple sequences can be
converted.

!!! IMPORTANT
=============
Do not attempt to mix formats, i.e. convert from a contact file format
to a sequence file format.

"""

__author__ = "Felix Simkovic"
__date__ = "01 Oct 2016"
__version__ = "0.1"

import argparse

import conkit.command_line
import conkit.io

logger = None


[docs]def main():
    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('infile')
    parser.add_argument('informat')
    parser.add_argument('outfile')
    parser.add_argument('outformat')
    args = parser.parse_args()

    # Setup the logger
    global logger
    logger = conkit.command_line.setup_logging(level='info')

    # Perform the conversion
    logger.info("Converting file\n\t%s of format %s\nto file\n\t%s of format %s",
                args.infile, args.informat, args.outfile, args.outformat)
    conkit.io.convert(args.infile, args.informat, args.outfile, args.outformat)

    return


if __name__ == "__main__":
    import sys 
    import traceback
    try:
        main()
        sys.exit(0)
    except Exception as e:
        if not isinstance(e, SystemExit):
            msg = "".join(traceback.format_exception(*sys.exc_info()))
            logger.critical(msg)
        sys.exit(1)