def test_full_LOC(self):
"""LOC should behave as expected when initialized with rich data"""
data = [
"abc\t def", " 3 \t n", " abc \txyz\n\n", "x\t5", "fgh ",
"x\t3 "
]
class rec(MappedRecord):
Required = {'abc': []}
maps = {'abc': list_adder, 'x': int_setter, 'fgh': bool_setter}
label_splitter = DelimitedSplitter('\t')
constructor = rec
strict = True
loc_bad = LineOrientedConstructor(data, label_splitter, maps,
constructor, strict)
self.assertRaises(FieldError, loc_bad)
strict = False
loc_good = LineOrientedConstructor(data, label_splitter, maps,
constructor, strict)
result = loc_good()
assert isinstance(result, rec)
self.assertEqual(result, {
'abc': ['def', 'xyz'],
'3': 'n',
'fgh': False,
'x': 3
})
def test_parsers(self):
"""DelimitedSplitter should return function with correct behavior"""
empty = DelimitedSplitter()
space = DelimitedSplitter(None)
semicolon = DelimitedSplitter(';')
twosplits = DelimitedSplitter(';', 2)
allsplits = DelimitedSplitter(';', None)
lastone = DelimitedSplitter(';', -1)
lasttwo = DelimitedSplitter(';', -2)
self.assertEqual(empty('a b c'), ['a', 'b c'])
self.assertEqual(empty('abc'), ['abc'])
self.assertEqual(empty(' '), [])
self.assertEqual(empty('a b c'), space('a b c'))
self.assertEqual(semicolon(' a ; b ; c d'), ['a', 'b ; c d'])
self.assertEqual(twosplits(' a ; b ; c d'), ['a', 'b', 'c d'])
self.assertEqual(allsplits(' a ; b ; c;;d;e ;'),
['a', 'b', 'c', '', 'd', 'e', ''])
self.assertEqual(lastone(' a ; b ; c;;d;e ;'),
['a ; b ; c;;d;e', ''])
self.assertEqual(lasttwo(' a ; b ; c;;d;e ;'),
['a ; b ; c;;d', 'e', ''])
self.assertEqual(lasttwo(''), [])
self.assertEqual(lasttwo('x'), ['x'])
self.assertEqual(lasttwo('x;'), ['x', ''])
def test_label_line_parser(self):
last_space = DelimitedSplitter(None, -1)
self.assertEquals(
_label_line_parser(StringIO('abc\tucag'), last_space), ({
"abc": ["ucag"]
}, ['abc']))
with self.assertRaises(ClustalFormatError):
_label_line_parser(StringIO('abctucag'), last_space)
def test_splitter(self):
"""StrictFieldWrapper with splitter should use that splitter"""
fields = ['label', 'count']
splitter = DelimitedSplitter(':', -1)
f = StrictFieldWrapper(fields, splitter)
self.assertEqual(f('n:k:n:a:sd '), {
'label': 'n:k:n:a',
'count': 'sd'
})
self.assertEqual(f('nknasd:'), {'label': 'nknasd', 'count': ''})
self.assertRaises(FieldError, f, '')
else:
result[key] = [val]
labels.append(key)
return result, labels
def _is_clustal_seq_line(line):
"""Returns True if line starts with a non-blank character but not 'CLUSTAL'
Useful for filtering other lines out of the file.
"""
return line and (not line[0].isspace()) and\
(not line.startswith('CLUSTAL')) and (not line.startswith('MUSCLE'))
last_space = DelimitedSplitter(None, -1)
def _delete_trailing_number(line):
"""Deletes trailing number from a line.
WARNING: does not preserve internal whitespace when a number is removed!
(converts each whitespace run to a single space). Returns the original
line if it didn't end in a number.
"""
pieces = line.split()
try:
int(pieces[-1])
return ' '.join(pieces[:-1])
except ValueError: # no trailing numbers
return line