class Test_NexusWriter_2(unittest.TestCase):
def setUp(self):
self.nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
self.nex.add(taxon, char, value)
def test_nexus_noninterleave(self):
"""Test Nexus Generation - Non-Interleaved"""
n = self.nex.make_nexus(interleave=False)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("MATRIX", n)
assert re.search("Latin\s+36", n)
assert re.search("French\s+14", n)
assert re.search("English\s+25", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s", n).groups()[0] == 'STANDARD'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";', n).groups()[0] == '123456'
def test_nexus_charblock(self):
"""Test Nexus Generation - with characters block"""
n = self.nex.make_nexus(charblock=True)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("CHARSTATELABELS", n)
assert re.search("1 char1,", n)
assert re.search("2 char2", n)
assert re.search("MATRIX", n)
assert re.search("Latin\s+36", n)
assert re.search("French\s+14", n)
assert re.search("English\s+25", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s", n).groups()[0] == 'STANDARD'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";', n).groups()[0] == '123456'
def test_nexus_interleave(self):
"""Test Nexus Generation - Interleaved"""
n = self.nex.make_nexus(interleave=True)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("MATRIX", n)
# char1
assert re.search("Latin\s+3", n)
assert re.search("French\s+1", n)
assert re.search("English\s+2", n)
# char2
assert re.search("Latin\s+6", n)
assert re.search("French\s+4", n)
assert re.search("English\s+5", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s", n).groups()[0] == 'STANDARD'
assert re.search("FORMAT.*(INTERLEAVE)", n).groups()[0] == 'INTERLEAVE'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";', n).groups()[0] == '123456'
def snpMatrixGenerator(sourceFile, destFile, recordAll=False,
recordRandomSample=True):
if recordAll == recordRandomSample:
print "Invalid Options"
exit()
destNexus = NexusWriter()
block = ""
snpCol = 0
for line in sourceFile:
if all(x in line.lower() for x in {"begin", "data"}):
sourceNexus = NexusReader()
sourceNexus.read_string(block)
if "data" in sourceNexus.blocks:
snpCol = _findDifferences(sourceNexus, destNexus, snpCol,
recordAll, recordRandomSample)
block = line
else:
block += line
sourceNexus = NexusReader()
sourceNexus.read_string(block)
if "data" in sourceNexus.blocks:
snpCol = _findDifferences(sourceNexus, destNexus, snpCol,
recordAll, recordRandomSample)
destFile.write(destNexus.make_nexus() + '\n')
destFile.close()
sourceFile.close()
def snpMatrixGenerator(sourceFile,
destFile,
recordAll=False,
recordRandomSample=True):
if recordAll == recordRandomSample:
print "Invalid Options"
exit()
destNexus = NexusWriter()
block = ""
snpCol = 0
for line in sourceFile:
if all(x in line.lower() for x in {"begin", "data"}):
sourceNexus = NexusReader()
sourceNexus.read_string(block)
if "data" in sourceNexus.blocks:
snpCol = _findDifferences(sourceNexus, destNexus, snpCol,
recordAll, recordRandomSample)
block = line
else:
block += line
sourceNexus = NexusReader()
sourceNexus.read_string(block)
if "data" in sourceNexus.blocks:
snpCol = _findDifferences(sourceNexus, destNexus, snpCol, recordAll,
recordRandomSample)
destFile.write(destNexus.make_nexus() + '\n')
destFile.close()
sourceFile.close()
def test_regression_format_string_has_quoted_symbols(self):
"""Regression: Symbols in the format string should be quoted"""
nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
nex.add(taxon, char, value)
out = nex.make_nexus()
assert 'SYMBOLS="123456"' in out
def test_regression_format_string_has_quoted_symbols(self):
"""Regression: Symbols in the format string should be quoted"""
nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
nex.add(taxon, char, value)
out = nex.make_nexus()
assert 'SYMBOLS="123456"' in out
def test_regression_format_string_has_datatype_first(self):
"""Regression: Format string should contain 'datatype' as the first element"""
# SplitsTree complains otherwise.
nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
nex.add(taxon, char, value)
out = nex.make_nexus()
assert "FORMAT DATATYPE=STANDARD" in out
def test_regression_format_string_has_datatype_first(self):
"""Regression: Format string should contain 'datatype' as the first element"""
# SplitsTree complains otherwise.
nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
nex.add(taxon, char, value)
out = nex.make_nexus()
assert "FORMAT DATATYPE=STANDARD" in out
class Test_NexusWriter(unittest.TestCase):
def setUp(self):
self.nex = NexusWriter()
for char in data:
for taxon, value in data[char].items():
self.nex.add(taxon, char, value)
def test_char_adding1(self):
"""Test Character Addition 1"""
assert self.nex.data['char1']['French'] == '1'
assert self.nex.data['char1']['English'] == '2'
assert self.nex.data['char1']['Latin'] == '3'
def test_char_adding2(self):
"""Test Character Addition 2"""
assert self.nex.data['char2']['French'] == '4'
assert self.nex.data['char2']['English'] == '5'
assert self.nex.data['char2']['Latin'] == '6'
def test_char_adding_integer(self):
"""Test Character Addition as integer"""
self.nex.add('French', 'char3', 9)
self.nex.add('English', 'char3', '9')
assert self.nex.data['char3']['French'] == '9'
assert self.nex.data['char3']['French'] == '9'
def test_characters(self):
assert 'char1' in self.nex.characters
assert 'char2' in self.nex.characters
def test_taxa(self):
assert 'French' in self.nex.taxa
assert 'English' in self.nex.taxa
assert 'Latin' in self.nex.taxa
def test_remove(self):
self.nex.remove("French", "char2")
assert 'French' not in self.nex.data['char2']
assert 'French' in self.nex.taxa
def test_remove_character(self):
self.nex.remove_character("char2")
assert len(self.nex.characters) == 1
assert 'char2' not in self.nex.data
def test_remove_taxon(self):
self.nex.remove_taxon("French")
assert 'French' not in self.nex.taxa
for char in self.nex.data:
assert 'French' not in self.nex.data[char]
n = self.nex.make_nexus(interleave=False)
assert re.search("DIMENSIONS NTAX=2 NCHAR=2;", n)
assert 'French' not in n
def test_nexus_noninterleave(self):
"""Test Nexus Generation - Non-Interleaved"""
n = self.nex.make_nexus(interleave=False)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("MATRIX", n)
assert re.search("Latin\s+36", n)
assert re.search("French\s+14", n)
assert re.search("English\s+25", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s", n).groups()[0] \
== 'STANDARD'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";', n).groups()[0] \
== '123456'
def test_nexus_charblock(self):
"""Test Nexus Generation - with characters block"""
n = self.nex.make_nexus(charblock=True)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("CHARSTATELABELS", n)
assert re.search("1 char1,", n)
assert re.search("2 char2", n)
assert re.search("MATRIX", n)
assert re.search("Latin\s+36", n)
assert re.search("French\s+14", n)
assert re.search("English\s+25", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s", n).groups()[0] \
== 'STANDARD'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";', n).groups()[0] \
== '123456'
def test_nexus_interleave(self):
"""Test Nexus Generation - Interleaved"""
n = self.nex.make_nexus(interleave=True)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("MATRIX", n)
# char1
assert re.search("Latin\s+3", n)
assert re.search("French\s+1", n)
assert re.search("English\s+2", n)
# char2
assert re.search("Latin\s+6", n)
assert re.search("French\s+4", n)
assert re.search("English\s+5", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s", n).groups()[0] == \
'STANDARD'
assert re.search("FORMAT.*(INTERLEAVE)", n).groups()[0] == \
'INTERLEAVE'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";', n).groups()[0] == \
'123456'
def test_polymorphic_characters(self):
self.nex.add("French", "char1", 2)
self.assertEqual(self.nex.data['char1']['French'], "12")
n = self.nex.make_nexus(charblock=True)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n) # no change
assert re.search("French\s+\(12\)4", n)
def test_write_to_file(self):
tmp = NamedTemporaryFile(delete=False, suffix=".nex")
tmp.close()
self.nex.write_to_file(tmp.name)
assert os.path.isfile(tmp.name)
with open(tmp.name, 'r') as handle:
n = handle.read()
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("MATRIX", n)
assert re.search("Latin\s+36", n)
assert re.search("French\s+14", n)
assert re.search("English\s+25", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s", n).groups()[0] \
== 'STANDARD'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";', n).groups()[0] \
== '123456'
os.unlink(tmp.name) # cleanup
def test_write_as_table(self):
content = self.nex.write_as_table()
assert re.search("Latin\s+36", content)
assert re.search("French\s+14", content)
assert re.search("English\s+25", content)
assert len(content.split("\n")) == 3
def test_write_as_table_with_polymorphoc(self):
self.nex.add('French', 'char1', '2')
content = self.nex.write_as_table()
assert re.search("Latin\s+36", content)
assert re.search("French\s+\(12\)4", content)
assert re.search("English\s+25", content)
assert len(content.split("\n")) == 3
class Test_NexusWriter_2(unittest.TestCase):
def setUp(self):
self.nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
self.nex.add(taxon, char, value)
def test_nexus_noninterleave(self):
"""Test Nexus Generation - Non-Interleaved"""
n = self.nex.make_nexus(interleave=False)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("MATRIX", n)
assert re.search("Latin\s+36", n)
assert re.search("French\s+14", n)
assert re.search("English\s+25", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s",
n).groups()[0] == 'STANDARD'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";',
n).groups()[0] == '123456'
def test_nexus_charblock(self):
"""Test Nexus Generation - with characters block"""
n = self.nex.make_nexus(charblock=True)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("CHARSTATELABELS", n)
assert re.search("1 char1,", n)
assert re.search("2 char2", n)
assert re.search("MATRIX", n)
assert re.search("Latin\s+36", n)
assert re.search("French\s+14", n)
assert re.search("English\s+25", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s",
n).groups()[0] == 'STANDARD'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";',
n).groups()[0] == '123456'
def test_nexus_interleave(self):
"""Test Nexus Generation - Interleaved"""
n = self.nex.make_nexus(interleave=True)
assert re.search("#NEXUS", n)
assert re.search("BEGIN DATA;", n)
assert re.search("DIMENSIONS NTAX=3 NCHAR=2;", n)
assert re.search("MATRIX", n)
# char1
assert re.search("Latin\s+3", n)
assert re.search("French\s+1", n)
assert re.search("English\s+2", n)
# char2
assert re.search("Latin\s+6", n)
assert re.search("French\s+4", n)
assert re.search("English\s+5", n)
assert re.search("FORMAT.*MISSING\=(.+?)", n).groups()[0] == '?'
assert re.search("FORMAT.*DATATYPE\=(\w+)\s",
n).groups()[0] == 'STANDARD'
assert re.search("FORMAT.*(INTERLEAVE)", n).groups()[0] == 'INTERLEAVE'
assert re.search('FORMAT.*SYMBOLS\="(\d+)";',
n).groups()[0] == '123456'