pdb_site_identity.py 文件源码

def main(argv, wayout):
    if not len(argv):
        argv.append('-h')
    parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__)
    parser.add_argument("-a","--alignment", help="multiple sequence alignment", required=True)
    parser.add_argument("-f","--format", default="fasta", help="alignment format [fasta]")
    parser.add_argument("-g","--gap-cutoff", default=0.5, type=float, help="minimum fraction of non-gap characters per site, else is called unconserved [0.5]")
    parser.add_argument("-i","--identity", action="store_true", help="report percent identity instead of score")
    parser.add_argument("-p","--pdb", help="PDB format file", required=True)
    parser.add_argument("-s","--sequence", help="sequence ID for PDB", required=True)
    args = parser.parse_args(argv)

    conservedict = get_alignment_conservation( args.alignment, args.format, args.sequence, args.gap_cutoff, args.identity)
    if conservedict: # indicating that the sequence was found and something was calculated
        rewrite_pdb(args.pdb, conservedict, wayout)
    else:
        sys.exit("# CANNOT CALCULATE CONSERVATION, EXITING")