def run(args):
write_output(shufflenexus(get_reader(args), args.numchars or False), args)
help="Number of Characters to Generate")
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
if options.numchars != False:
try:
options.numchars = int(options.numchars)
except ValueError:
print "numchars needs to be a number!"
raise
nexus = NexusReader(nexusname)
nexus = shufflenexus(nexus, options.numchars)
if newnexus is not None:
nexus.write_to_file(newnexus)
print "New random nexus written to %s" % newnexus
else:
print nexus.write()
def test_resample_100(self):
nexus_obj = shufflenexus(self.nexus_obj, 100)
assert len(nexus_obj.characters) == 100
assert sorted(nexus_obj.taxalist) == ['George', 'John', 'Paul', 'Ringo']
help="Number of Characters to Generate")
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
if options.numchars != False:
try:
options.numchars = int(options.numchars)
except ValueError:
print("numchars needs to be a number!")
raise
nexus = NexusReader(nexusname)
nexus = shufflenexus(nexus, options.numchars)
if newnexus is not None:
nexus.write_to_file(newnexus)
print("New random nexus written to %s" % newnexus)
else:
print(nexus.write())
def test_output(self):
nexus_obj = shufflenexus(self.nexus_obj)
assert isinstance(nexus_obj, NexusWriter)
