def test_combine_missing(nex1, nex3):
newnex = combine_nexuses(nex1, nex3)
print(newnex.data)
assert newnex.data['0.1']['Harry'] == '1'
assert newnex.data['0.1']['Simon'] == '2'
assert newnex.data['2.1']['Betty'] == '3'
assert newnex.data['2.1']['Boris'] == '4'
def test_combine_with_character_labels(self):
n1 = NexusReader()
n1.read_string(
"""
BEGIN DATA;
DIMENSIONS NTAX=3 NCHAR=3;
FORMAT DATATYPE=STANDARD MISSING=0 GAP=- SYMBOLS="123";
CHARSTATELABELS
1 char1,
2 char2,
3 char3
;
MATRIX
Tax1 123
Tax2 123
Tax3 123
;
"""
)
n2 = NexusReader()
n2.read_string(
"""
BEGIN DATA;
DIMENSIONS NTAX=3 NCHAR=3;
FORMAT DATATYPE=STANDARD MISSING=0 GAP=- SYMBOLS="456";
CHARSTATELABELS
1 char1,
2 char2,
3 char3
;
MATRIX
Tax1 456
Tax2 456
Tax3 456
;
"""
)
newnex = combine_nexuses([n1, n2])
assert re.search(r"""\bNTAX=3\b""", newnex.write())
assert re.search(r"""\bNCHAR=6\b""", newnex.write())
assert re.search(r'\sSYMBOLS="123456"[\s;]', newnex.write())
for tax in [1, 2, 3]:
assert re.search(r"""\bTax%d\s+123456\b""" % tax, newnex.write())
counter = 1
for nex_id in [1, 2]:
for char_id in [1, 2, 3]:
assert re.search(
r"""\b%d\s+%d.char%d\b""" % (counter, nex_id, char_id),
newnex.write(charblock=True)
)
counter += 1
def test_combine():
nex1 = NexusReader.from_string("""Begin trees;
tree 1 = (a,b,c);
end;""")
nex2 = NexusReader.from_string("""Begin trees;
tree 2 = (b,a,c);
tree 3 = (b,c,a);
end;""")
newnex = combine_nexuses([nex1, nex2])
assert len(newnex.trees) == 3
assert newnex.trees[0] == "tree 1 = (a,b,c);"
assert newnex.trees[1] == "tree 2 = (b,a,c);"
assert newnex.trees[2] == "tree 3 = (b,c,a);"
def test_combine_with_character_labels(self):
n1 = NexusReader()
n1.read_string("""
BEGIN DATA;
DIMENSIONS NTAX=3 NCHAR=3;
FORMAT DATATYPE=STANDARD MISSING=0 GAP=- SYMBOLS="123";
CHARSTATELABELS
1 char1,
2 char2,
3 char3
;
MATRIX
Tax1 123
Tax2 123
Tax3 123
;
""")
n2 = NexusReader()
n2.read_string("""
BEGIN DATA;
DIMENSIONS NTAX=3 NCHAR=3;
FORMAT DATATYPE=STANDARD MISSING=0 GAP=- SYMBOLS="456";
CHARSTATELABELS
1 char1,
2 char2,
3 char3
;
MATRIX
Tax1 456
Tax2 456
Tax3 456
;
""")
newnex = combine_nexuses([n1, n2])
assert re.search(r"""\bNTAX=3\b""", newnex.write())
assert re.search(r"""\bNCHAR=6\b""", newnex.write())
assert re.search(r'\sSYMBOLS="123456"[\s;]', newnex.write())
for tax in [1, 2, 3]:
assert re.search(r"""\bTax%d\s+123456\b""" % tax, newnex.write())
counter = 1
for nex_id in [1, 2]:
for char_id in [1, 2, 3]:
assert re.search(
r"""\b%d\s+%d.char%d\b""" % (counter, nex_id, char_id),
newnex.write(charblock=True))
counter += 1
def test_combine_missing_generated_formatline(self):
newnex = combine_nexuses([self.nex1, self.nex3]).write()
assert re.search(r"""\bNTAX=4\b""", newnex)
assert re.search(r"""\bNCHAR=2\b""", newnex)
assert re.search(r'\sSYMBOLS="12345"[\s;]', newnex)
def test_combine_missing_generated_matrix(self):
newnex = combine_nexuses([self.nex1, self.nex3]).write()
assert re.search(r"""\bSimon\s+25\b""", newnex)
assert re.search(r"""\bHarry\s+1\\?\b""", newnex)
assert re.search(r"""\bBetty\s+\?3\b""", newnex)
assert re.search(r"""\bBoris\s+\?4\b""", newnex)
def test_combine_missing(self):
newnex = combine_nexuses([self.nex1, self.nex3])
assert newnex.data['0.1']['Harry'] == '1'
assert newnex.data['0.1']['Simon'] == '2'
assert newnex.data['2.1']['Betty'] == '3'
assert newnex.data['2.1']['Boris'] == '4'
def test_combine_simple_generated_matrix(self):
newnex = combine_nexuses([self.nex1, self.nex2]).write()
assert re.search(r"""\bSimon\s+24\b""", newnex)
assert re.search(r"""\bHarry\s+13\b""", newnex)
def test_combine_simple(self):
newnex = combine_nexuses([self.nex1, self.nex2])
assert newnex.data['0.1']['Harry'] == '1'
assert newnex.data['0.1']['Simon'] == '2'
assert newnex.data['2.1']['Harry'] == '3'
assert newnex.data['2.1']['Simon'] == '4'
def test_combine_missing_generated_formatline(self):
newnex = combine_nexuses([self.nex1, self.nex3])
assert re.search(r"""\bNTAX=4\b""", newnex.write())
assert re.search(r"""\bNCHAR=2\b""", newnex.write())
assert re.search(r'\sSYMBOLS="12345"[\s;]', newnex.write())
def test_combine_missing_generated_matrix(self):
newnex = combine_nexuses([self.nex1, self.nex3])
assert re.search(r"""\bSimon\s+25\b""", newnex.write())
assert re.search(r"""\bHarry\s+1\\?\b""", newnex.write())
assert re.search(r"""\bBetty\s+\?3\b""", newnex.write())
assert re.search(r"""\bBoris\s+\?4\b""", newnex.write())
def test_combine_missing(self):
newnex = combine_nexuses([self.nex1, self.nex3])
assert newnex.data['1.1']['Harry'] == '1'
assert newnex.data['1.1']['Simon'] == '2'
assert newnex.data['2.1']['Betty'] == '3'
assert newnex.data['2.1']['Boris'] == '4'
def test_combine_simple_generated_matrix(self):
newnex = combine_nexuses([self.nex1, self.nex2])
assert re.search(r"""\bSimon\s+24\b""", newnex.write())
assert re.search(r"""\bHarry\s+13\b""", newnex.write())
def test_combine_simple(self):
newnex = combine_nexuses([self.nex1, self.nex2])
assert newnex.data['1.1']['Harry'] == '1'
assert newnex.data['1.1']['Simon'] == '2'
assert newnex.data['2.1']['Harry'] == '3'
assert newnex.data['2.1']['Simon'] == '4'
def test_combine_iterated(nex1):
res = combine_nexuses(combine_nexuses(nex1))
assert res
def test_combine_simple_generated_formatline(nex1, nex2):
newnex = combine_nexuses([nex1, nex2]).write()
assert re.search(r"""\bNTAX=2\b""", newnex)
assert re.search(r"""\bNCHAR=2\b""", newnex)
assert re.search(r'\sSYMBOLS="1234"[\s;]', newnex)
