def test_find_unique_sites_2(self):
nexus = NexusReader()
nexus.read_string("""Begin data;
Dimensions ntax=4 nchar=7;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 10000?-
Simon 1100011
Betty 1110000
Louise 1111000
;""")
unique = find_unique_sites(nexus)
# site 1 should NOT be in the uniques (3x1 and 1x0)
# - i.e. are we ignoring sites with ONE absent taxon
assert 1 not in unique
# these should also NOT be in unique
assert 0 not in unique
assert 2 not in unique
assert 4 not in unique # constant
# site 3 is a simple unique site - check we found it
assert 3 in unique
# sites 5 and 6 should also be unique
# - are we handling missing data appropriately?
assert 5 in unique
assert 6 in unique
def test_find_unique_sites_2(self):
nexus = NexusReader()
nexus.read_string("""Begin data;
Dimensions ntax=4 nchar=7;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 10000?-
Simon 1100011
Betty 1110000
Louise 1111000
;""")
unique = find_unique_sites(nexus)
# site 1 should NOT be in the uniques (3x1 and 1x0)
# - i.e. are we ignoring sites with ONE absent taxon
assert 1 not in unique
# these should also NOT be in unique
assert 0 not in unique
assert 2 not in unique
assert 4 not in unique # constant
# site 3 is a simple unique site - check we found it
assert 3 in unique
# sites 5 and 6 should also be unique
# - are we handling missing data appropriately?
assert 5 in unique
assert 6 in unique
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)
print("New nexus written to %s" % newnexusname)
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)
print("New nexus written to %s" % newnexusname)
def test_find_unique_sites_1(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
assert len(find_unique_sites(nexus)) == 0
def test_find_unique_sites_1(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
assert not find_unique_sites(nexus)
