#!/home/jenkins/workspace/ccpem/ccp-em_centos5/devtools/install/devbin/python

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

import argparse
import conkit
import logging
import sys

logging.basicConfig(format='%(message)s', level=logging.INFO)


def main():
    text = """
Analyse a Multiple Sequence Alignment

File format options are:

    Sequence files: [{0}]

"""
    options = sorted(conkit.io.SEQUENCE_FILE_PARSERS.keys())
    text = text.format(' '.join(options))
    parser = argparse.ArgumentParser(description=text, formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('-id', default=0.7, type=float, help='sequence identity [default: 0.7]')
    parser.add_argument('msafile')
    parser.add_argument('msaformat')
    args = parser.parse_args()
    
    # Compute all the data
    hierarchy = conkit.io.read(args.msafile, args.msaformat)
    seq_len = hierarchy.top_sequence.seq_len
    nseqs = hierarchy.nseqs
    meff = hierarchy.calculate_meff(identity=args.id)
    
    logging.info('File: {0}'.format(args.msafile))
    logging.info('Format: {0}'.format(args.msaformat))
    logging.info('Seq ID: {0}'.format(args.id))
    logging.info('Seq Len: {0}'.format(seq_len))
    logging.info('N seqs: {0}'.format(nseqs))
    logging.info('M eff: {0}'.format(meff))


if __name__ == "__main__":
    sys.exit(main())