Source code for conkit.command_line.conkit_msatool

#!/usr/bin/env python
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"""This script analyses a Multiple Sequence Alignment.

It provides you estimates about the quality, which will allow
you to determine its usefulness for covariance-based contact
prediction.

"""

__author__ = "Felix Simkovic"
__date__ = "21 Nov 2016"
__version__ = "0.1"

import argparse

import conkit.command_line
import conkit.io
import conkit.plot

logger = None


[docs]def main():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('msafile', help='Multiple Sequence Alignment file')
    parser.add_argument('msaformat', help='Multiple Sequence Alignment format')
    args = parser.parse_args()

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

    # Compute all the data
    msa = conkit.io.read(args.msafile, args.msaformat)
    plot = args.msafile.rsplit('.', 1)[0] + '.png'
    conkit.plot.SequenceCoverageFigure(msa, file_name=plot)

    logger.info('Input MSA File:                            %s', args.msafile)
    logger.info('Input MSA Format:                          %s', args.msaformat)
    logger.info('Length of the Target Sequence:             %d',
                msa.top_sequence.seq_len)
    logger.info('Total Number of Sequences:                 %d', msa.nseq)
    logger.info('Number of Effective Sequences:             %d', msa.neff)
    logger.info('Sequence Coverage Plot:                    %s', plot)


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)