#!/usr/bin/env python
import sys
from nexus import NexusReader, VERSION
__author__ = 'Simon Greenhill <simon@simon.net.nz>'
__doc__ = """deinterleave - python-nexus tools v%(version)s
Converts an interleaved nexus to a simple nexus.
""" % {'version': VERSION,}

if __name__ == '__main__':
    #set up command-line options
    from optparse import OptionParser
    parser = OptionParser(usage="usage: %prog fudge.nex output.nex")
    options, args = parser.parse_args()
    
    try:
        nexusname = args[0]
    except IndexError:
        print __doc__
        print "Author: %s\n" % __author__
        parser.print_help()
        sys.exit()
    
    try:
        newnexus = args[1]
    except IndexError:
        newnexus = None
        
    nexus = NexusReader(nexusname)
    
    if newnexus is not None:
        nexus.write_to_file(newnexus)
        print "New nexus written to %s" % newnexus
    else:
        print nexus.write()