Beispiel #1
0
 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_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
Beispiel #3
0
 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
Beispiel #4
0
    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']