class Test_DataHandler_NoMissingInSymbols(unittest.TestCase):
"""
Regression:
Test that the missing or gap symbols are NOT in the SYMBOLS format string
"""
def test_write(self):
self.nex = NexusReader()
self.nex.read_string("""
#NEXUS
begin data;
Dimensions ntax=2 nchar=2;
Format datatype=standard gap=- symbols="01";
Matrix
Harry 1-
Simon 0?
;
End;
""")
expected_patterns = [
'^begin data;$',
'^\s+dimensions ntax=2 nchar=2;$',
'^\s+format datatype=standard gap=- symbols="01";$',
"^matrix$",
"^Harry\s+1-",
"^Simon\s+0\?$",
'^\s+;$',
'^end;$',
]
written = self.nex.write()
for expected in expected_patterns:
assert re.search(expected, written, re.MULTILINE), \
'Expected "%s"' % expected
def test_read_string(self):
handle = open(os.path.join(EXAMPLE_DIR, 'example.nex'))
data = handle.read()
handle.close()
nex = NexusReader()
nex.read_string(data)
assert 'data' in nex.blocks
assert 'Simon' in nex.blocks['data'].matrix
def test_write_produces_end(self):
nex = NexusReader()
nex.read_string("""
begin assumptions;
A = 1;
end;
""")
assert "end;" in nex.write()
def test_generic_readwrite(self):
expected = [
"begin sets;",
" A = 1;",
" B = 2;",
"end;",
]
nex = NexusReader()
nex.read_string("\n".join(expected))
for line in nex.sets.write().split("\n"):
e = expected.pop(0).strip()
assert line.strip() == e
def test_labelled_unrooted(self):
nex = NexusReader()
nex.read_string("""
#NEXUS
begin trees;
translate
0 Tom,
1 Simon,
2 Fred;
tree unrooted [U] = (0,1,2);
end;
""")
assert len(nex.trees.trees) == 1
assert nex.trees.trees == ['tree unrooted [U] = (0,1,2);']
def test_treelabel(self):
nex = NexusReader()
nex.read_string("""
#NEXUS
begin trees;
translate
0 Tom,
1 Simon,
2 Fred;
tree TREEONE = (0,1,2);
end;
""")
assert len(nex.trees.trees) == 1
assert nex.trees.trees == ['tree TREEONE = (0,1,2);']
def test_ok_starting_with_one(self):
nex = NexusReader()
nex.read_string("""
#NEXUS
begin trees;
translate
1 Tom,
2 Simon,
3 Fred;
tree tree = (1,2,3)
end;
""")
assert len(nex.trees.translators) == 3
assert '1' in nex.trees.translators
assert '2' in nex.trees.translators
assert '3' in nex.trees.translators
def test_ok_starting_with_zero(self):
nex = NexusReader()
nex.read_string("""
#NEXUS
begin trees;
translate
0 Tom,
1 Simon,
2 Fred;
tree tree = (0,1,2)
end;
""")
assert len(nex.trees.translators) == 3
assert '0' in nex.trees.translators
assert '1' in nex.trees.translators
assert '2' in nex.trees.translators
class Test_DataHandler_Regression_Mesquite(unittest.TestCase):
"""Regression: Test that we can parse MESQUITE data blocks"""
def setUp(self):
self.nex = NexusReader()
self.nex.read_string("""
#NEXUS
Begin data;
TITLE Untitled_Block_of_Taxa;
LINK Taxa = Untitled_Block_of_Taxa;
Dimensions ntax=2 nchar=2;
Format datatype=standard gap=- symbols="01";
Matrix
Harry 00
Simon 01
;
End;
""")
def test_attributes(self):
assert len(self.nex.data.attributes) == 2
assert self.nex.data.attributes[0] == \
"""TITLE Untitled_Block_of_Taxa;"""
assert self.nex.data.attributes[1] == \
"""LINK Taxa = Untitled_Block_of_Taxa;"""
def test_write(self):
expected_patterns = [
'^begin data;$',
'^\s+TITLE Untitled_Block_of_Taxa;$',
'^\s+LINK Taxa = Untitled_Block_of_Taxa;$',
'^\s+dimensions ntax=2 nchar=2;$',
'^\s+format datatype=standard gap=- symbols="01";$',
"^matrix$",
"^Harry\s+00",
"^Simon\s+01$",
'^\s+;$',
'^end;$',
]
written = self.nex.write()
for expected in expected_patterns:
assert re.search(expected, written, re.MULTILINE), \
'Expected "%s"' % expected
