def test_find_constant_sites_2(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, 'example2.nex'))
const = find_constant_sites(nexus)
assert len(const) == 4
assert 0 in const
assert 1 in const
assert 2 in const
assert 3 in const
newnexusname = args[1]
except IndexError:
newnexusname = None
nexus = NexusReader(nexusname)
newnexus = None
if options.number:
if newnexusname is not None:
print_site_values(nexus, newnexusname)
else:
print_site_values(nexus)
elif options.constant:
const = find_constant_sites(nexus)
newnexus = new_nexus_without_sites(nexus, const)
print("Constant Sites: %s" % ",".join([str(i) for i in const]))
elif options.unique:
unique = find_unique_sites(nexus)
newnexus = new_nexus_without_sites(nexus, unique)
print("Unique Sites: %s" % ",".join([str(i) for i in unique]))
elif options.stats:
d = print_character_stats(nexus)
else:
exit()
# check for saving
if newnexus is not None and newnexusname is not None:
newnexus.write_to_file(newnexusname)
def test_find_constant_sites_1(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
assert len(find_constant_sites(nexus)) == 0
try:
newnexusname = args[1]
except IndexError:
newnexusname = None
nexus = NexusReader(nexusname)
newnexus = None
if options.number:
if newnexusname is not None:
print_site_values(nexus, newnexusname)
else:
print_site_values(nexus)
elif options.constant:
const = find_constant_sites(nexus)
newnexus = new_nexus_without_sites(nexus, const)
print("Constant Sites: %s" % ",".join([str(i) for i in const]))
elif options.unique:
unique = find_unique_sites(nexus)
newnexus = new_nexus_without_sites(nexus, unique)
print("Unique Sites: %s" % ",".join([str(i) for i in unique]))
elif options.stats:
d = print_character_stats(nexus)
else:
exit()
# check for saving
if newnexus is not None and newnexusname is not None:
newnexus.write_to_file(newnexusname)