#!/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())