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
class Test_TreeHandler_Regression_Mesquite(unittest.TestCase):
"""Regression: Test that we can parse MESQUITE taxa blocks"""
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'mesquite_formatted_branches.trees')
)
def test_attributes(self):
assert len(self.nex.trees.attributes) == 2
assert self.nex.trees.attributes[0] == \
"""Title 'Trees from "temp.trees"';"""
assert self.nex.trees.attributes[1] == \
"""LINK Taxa = Untitled_Block_of_Taxa;"""
def test_found_trees(self):
assert self.nex.trees.ntrees == 1
def test_found_taxa(self):
assert len(self.nex.trees.taxa) == 3
assert 'A' in self.nex.trees.taxa
assert 'B' in self.nex.trees.taxa
assert 'C' in self.nex.trees.taxa
def test_was_translated(self):
assert self.nex.trees.was_translated
def test_translation(self):
assert self.nex.trees.translators['1'] == 'A'
assert self.nex.trees.translators['2'] == 'B'
assert self.nex.trees.translators['3'] == 'C'
def test_write(self):
written = self.nex.write()
assert """Title 'Trees from "temp.trees"';""" in written
assert """LINK Taxa = Untitled_Block_of_Taxa;""" in written
def test_write_produces_end(self):
nex = NexusReader()
nex.read_string("""
begin assumptions;
A = 1;
end;
""")
assert "end;" in nex.write()
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
class Test_TaxaHandler_Regression_Mesquite(unittest.TestCase):
"""Regression: Test that we can parse MESQUITE taxa blocks"""
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'mesquite_taxa_block.nex')
)
def test_taxa_block(self):
for taxon in ['A', 'B', 'C']:
assert taxon in self.nex.taxa
# did we get the right number of taxa in the matrix?
assert self.nex.taxa.ntaxa == len(self.nex.taxa.taxa) == 3
def test_taxa_block_attributes(self):
assert 'taxa' in self.nex.blocks
assert len(self.nex.taxa.attributes) == 2
assert 'TITLE Untitled_Block_of_Taxa;' in self.nex.taxa.attributes
assert 'LINK Taxa = Untitled_Block_of_Taxa;' in \
self.nex.taxa.attributes
def test_write(self):
expected_patterns = [
'^begin taxa;$',
'^\s+TITLE Untitled_Block_of_Taxa;$',
'^\s+dimensions ntax=3;$',
'^\s+taxlabels$',
"^\s+\[1\] A$",
"^\s+\[2\] B$",
"^\s+\[3\] C$",
'^;$',
'^end;$',
]
written = self.nex.write()
for expected in expected_patterns:
assert re.search(expected, written, re.MULTILINE), \
'Expected "%s"' % expected
def test_write(examples):
nex = NexusReader(examples / 'example.trees')
assert nex.write().startswith('#NEXUS')
assert examples.joinpath('example.trees').read_text(
encoding='utf8') == nex.write()
def test_roundtrip(examples):
nex = NexusReader(examples.joinpath('example2.nex'))
_ = NexusReader.from_string(nex.write())
def test_write(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example.trees'))
with open(os.path.join(EXAMPLE_DIR, 'example.trees')) as handle:
text = handle.read()
assert text == nex.write()