예제 #1
0
            for w in wrapper.wrap(s):
                print w
        print
    return
    

if __name__ == '__main__':
    from optparse import OptionParser
    parser = OptionParser(usage="usage: %prog [taxa/sites] nexus.nex")
    options, commands = parser.parse_args()
    
    if len(commands) != 2:
        print __doc__
        parser.print_help()
        quit()
    
    command, nex = commands
    
    try:
        nex = NexusReader(nex)
    except IOError:
        raise IOError("Unable to read %s" % nex)
        
    if command in ('taxa', 't'):
        tally = tally_by_taxon(nex)
    elif command in ('site', 's'):
        tally = tally_by_site(nex)
    else:
        quit("Invalid tally command. Only 'taxa' and 'site' are valid.")
    
    print_tally(tally)
예제 #2
0
    for i in sorted(tally):
        print("%d\t%d" % (i, tally[i]))
    return

if __name__ == '__main__':
    from optparse import OptionParser
    parser = OptionParser(usage="usage: %prog [taxa/sites/binary] nexus.nex")
    options, commands = parser.parse_args()

    if len(commands) != 2:
        print(__doc__)
        print("Author: %s\n" % __author__)
        parser.print_help()
        quit()

    command, nex = commands

    try:
        nex = NexusReader(nex)
    except IOError:
        raise IOError("Unable to read %s" % nex)

    if command in ('taxa', 't'):
        print_tally(tally_by_taxon(nex))
    elif command in ('site', 's'):
        print_tally(tally_by_site(nex))
    elif command in ('binary', 'b'):
        print_binary(count_binary_set_size(nex))
    else:
        quit("Invalid tally command. Only 'taxa' and 'site' are valid.")
예제 #3
0
            for w in wrapper.wrap(s):
                print w
        print
    return


if __name__ == '__main__':
    from optparse import OptionParser
    parser = OptionParser(usage="usage: %prog [taxa/sites] nexus.nex")
    options, commands = parser.parse_args()

    if len(commands) != 2:
        print __doc__
        parser.print_help()
        quit()

    command, nex = commands

    try:
        nex = NexusReader(nex)
    except IOError:
        raise IOError("Unable to read %s" % nex)

    if command in ('taxa', 't'):
        tally = tally_by_taxon(nex)
    elif command in ('site', 's'):
        tally = tally_by_site(nex)
    else:
        quit("Invalid tally command. Only 'taxa' and 'site' are valid.")

    print_tally(tally)
예제 #4
0
        print("%d\t%d" % (i, tally[i]))
    return


if __name__ == '__main__':
    from optparse import OptionParser
    parser = OptionParser(usage="usage: %prog [taxa/sites/binary] nexus.nex")
    options, commands = parser.parse_args()

    if len(commands) != 2:
        print(__doc__)
        print("Author: %s\n" % __author__)
        parser.print_help()
        quit()

    command, nex = commands

    try:
        nex = NexusReader(nex)
    except IOError:
        raise IOError("Unable to read %s" % nex)

    if command in ('taxa', 't'):
        print_tally(tally_by_taxon(nex))
    elif command in ('site', 's'):
        print_tally(tally_by_site(nex))
    elif command in ('binary', 'b'):
        print_binary(count_binary_set_size(nex))
    else:
        quit("Invalid tally command. Only 'taxa' and 'site' are valid.")