def test_parse_format_line_returns_none(self):
d = DataHandler()
assert d.parse_format_line('#NEXUS ') is None
assert d.parse_format_line('') is None
assert d.parse_format_line('Begin data;') is None
assert d.parse_format_line('Dimensions ntax=4 nchar=2;') is None
assert d.parse_format_line('Matrix') is None
assert d.parse_format_line('Harry 00') is None
assert d.parse_format_line('Simon 01') is None
assert d.parse_format_line('Betty 10') is None
assert d.parse_format_line('Louise 11') is None
assert d.parse_format_line(' ;') is None
assert d.parse_format_line('End;') is None
def test_parse_format_line(self):
d = DataHandler()
f = d.parse_format_line('Format datatype=standard symbols="01" gap=-;')
assert f['datatype'] == 'standard', "Expected 'standard', but got '%s'" % f['datatype']
assert f['symbols'] == '01', "Expected '01', but got '%s'" % f['symbols']
assert f['gap'] == '-', "Expected 'gap', but got '%s'" % f['gap']
f = d.parse_format_line('FORMAT datatype=RNA missing=? gap=- symbols="ACGU" labels interleave;')
assert f['datatype'] == 'rna', "Expected 'rna', but got '%s'" % f['datatype']
assert f['missing'] == '?', "Expected '?', but got '%s'" % f['missing']
assert f['gap'] == '-', "Expected '-', but got '%s'" % f['gap']
assert f['symbols'] == 'acgu', "Expected 'acgu', but got '%s'" % f['symbols']
assert f['labels'] == True, "Expected <True>, but got '%s'" % f['labels']
assert f['interleave'] == True, "Expected <True>, but got '%s'" % f['interleave']
def test_parse_format_line(self):
d = DataHandler()
f = d.parse_format_line('Format datatype=standard gap=- symbols="01";')
assert f['datatype'] == 'standard', \
"Expected 'standard', but got '%s'" % f['datatype']
assert f['symbols'] == '01', \
"Expected '01', but got '%s'" % f['symbols']
assert f['gap'] == '-', \
"Expected 'gap', but got '%s'" % f['gap']
fmt = 'FORMAT datatype=RNA missing=? symbols="ACGU" labels interleave;'
f = d.parse_format_line(fmt)
assert f['datatype'] == 'rna', \
"Expected 'rna', but got '%s'" % f['datatype']
assert f['missing'] == '?', \
"Expected '?', but got '%s'" % f['missing']
assert f['symbols'] == 'acgu', \
"Expected 'acgu', but got '%s'" % f['symbols']
assert f['labels'] is True, \
"Expected <True>, but got '%s'" % f['labels']
assert f['interleave'] is True, \
"Expected <True>, but got '%s'" % f['interleave']
def test_maddison(self):
assert DataHandler()._parse_sites('TAG;') == ['T', 'A', 'G']
def test_extra_comma(self):
assert DataHandler()._parse_sites('(T,A),C,G') == ['T,A', 'C', 'G']
def test_comma(self):
assert DataHandler()._parse_sites('123(4,5)56') == \
['1', '2', '3', '4,5', '5', '6']
def test_sequence(self):
assert DataHandler()._parse_sites("ACGTU?") == \
['A', 'C', 'G', 'T', 'U', '?']
def test_multi(self):
assert DataHandler()._parse_sites('1(12)') == ['1', '12']
def test_simple(self):
assert DataHandler()._parse_sites('123') == ['1', '2', '3']
def test_parse_format_line_returns_none(self):
d = DataHandler()
assert d.parse_format_line('#NEXUS ') is None
assert d.parse_format_line('') is None
assert d.parse_format_line('Begin data;') is None
assert d.parse_format_line('Dimensions ntax=4 nchar=2;') is None
assert d.parse_format_line('Matrix') is None
assert d.parse_format_line('Harry 00') is None
assert d.parse_format_line('Simon 01') is None
assert d.parse_format_line('Betty 10') is None
assert d.parse_format_line('Louise 11') is None
assert d.parse_format_line(' ;') is None
assert d.parse_format_line('End;') is None
def test_parse_range():
d = DataHandler()
assert d.parse_range("1-3") == [1, 2, 3]
assert d.parse_range("29") == [29]
assert d.parse_range("1,9") == [1, 9]
def test_DataHandler_parse_sites(input, expected):
assert DataHandler()._parse_sites(input) == expected