def test_count_other_values_two(self):
expected = {
'Harry': 1,
'Simon': 2,
'Peter': 1,
'Betty': 0,
'Louise': 0
}
nexus = NexusReader()
nexus.read_string("""#NEXUS
Begin data;
Dimensions ntax=5 nchar=3;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 0A0 [No missing]
Simon 0AB [one missing]
Peter 0-B [one gap]
Betty ?-1 [one gap and one missing = 2 missing]
Louise ??? [three missing]
;
End;
""")
count = count_site_values(nexus, ['A', 'B'])
for taxon in count:
assert count[taxon] == expected[taxon]
def print_site_values(nexus_obj, characters=['-', '?']):
"""
Prints out counts of the number of sites with state in `characters` in a
nexus.
(Wrapper around `count_site_values`)
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
"""
count = count_site_values(nexus_obj, characters)
print ("Number of %s in %s" % (",".join(characters), nexus_obj.filename))
for taxon in sorted(count):
prop = (count[taxon] / nexus.data.nchar) * 100
print(
"%s: %d/%d (%0.2f%%)" %
(taxon.ljust(20), count[taxon], nexus.data.nchar, prop)
)
print('-' * 76)
total_count = sum([x for x in count.values()])
total_data = nexus.data.nchar * nexus.data.ntaxa
prop = (total_count / total_data) * 100
print('TOTAL: %d/%d (%0.2f%%)' %
(total_count, total_data, prop)
)
def print_site_values(nexus_obj, characters=None):
"""
Prints out counts of the number of sites with state in `characters` in a
nexus.
(Wrapper around `count_site_values`)
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
"""
characters = characters if characters is not None else ['-', '?']
count = count_site_values(nexus_obj, characters)
print("Number of %s in %s" % (",".join(characters), nexus_obj.filename))
for taxon in sorted(count):
prop = (count[taxon] / nexus.data.nchar) * 100
print(
"%s: %d/%d (%0.2f%%)" %
(taxon.ljust(20), count[taxon], nexus.data.nchar, prop)
)
print('-' * 76)
total_count = sum([x for x in count.values()])
total_data = nexus.data.nchar * nexus.data.ntaxa
prop = (total_count / total_data) * 100
print('TOTAL: %d/%d (%0.2f%%)' %
(total_count, total_data, prop)
)
def test_count_missing_two():
expected = {'Harry': 0, 'Simon': 1, 'Peter': 1, 'Betty': 2, 'Louise': 3}
nexus = NexusReader.from_string("""#NEXUS
Begin data;
Dimensions ntax=5 nchar=3;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 010 [No missing]
Simon 0?0 [one missing]
Peter 0-0 [one gap]
Betty ?-1 [one gap and one missing = 2 missing]
Louise ??? [three missing]
;
End;
""")
missing = count_site_values(nexus)
for taxon in missing:
assert missing[taxon] == expected[taxon]
def test_count_other_values_two(self):
expected = {"Harry": 1, "Simon": 2, "Peter": 1, "Betty": 0, "Louise": 0}
nexus = NexusReader()
nexus.read_string(
"""#NEXUS
Begin data;
Dimensions ntax=5 nchar=3;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 0A0 [No missing]
Simon 0AB [one missing]
Peter 0-B [one gap]
Betty ?-1 [one gap and one missing = 2 missing]
Louise ??? [three missing]
;
End;
"""
)
count = count_site_values(nexus, ["A", "B"])
for taxon in count:
assert count[taxon] == expected[taxon]
def test_count_other_values_one(self):
expected = {
'Harry': 1, 'Simon': 1, 'Peter': 0, 'Betty': 0, 'Louise': 0
}
nexus = NexusReader()
nexus.read_string("""#NEXUS
Begin data;
Dimensions ntax=5 nchar=3;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 0A0 [No missing]
Simon 0A0 [one missing]
Peter 0-0 [one gap]
Betty ?-1 [one gap and one missing = 2 missing]
Louise ??? [three missing]
;
End;
""")
count = count_site_values(nexus, 'A')
for taxon in count:
assert count[taxon] == expected[taxon]
def test_count_missing_one(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, "example.nex"))
missing = count_site_values(nexus)
for taxon in missing:
assert missing[taxon] == 0
def test_count_missing_one(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
missing = count_site_values(nexus)
for taxon in missing:
assert missing[taxon] == 0
def test_errorcheck_characters(nex):
with pytest.raises(TypeError):
count_site_values(nex, None)
def test_count_missing_one(nex):
missing = count_site_values(nex)
for taxon in missing:
assert missing[taxon] == 0