def test_bad(self):
"""Should reject bad data if strict"""
result = parse_clustal(BAD, strict=False)
self.assertEqual(dict(result), {})
# should fail unless we turned strict processing off
with self.assertRaises(RecordError):
dict(parse_clustal(BAD))
def test_bad(self):
"""Should reject bad data if strict"""
result = parse_clustal(BAD, strict=False)
self.assertEqual(dict(result), {})
# should fail unless we turned strict processing off
with self.assertRaises(RecordError):
dict(parse_clustal(BAD))
def test_real(self):
"""Should handle real Clustal output"""
data = parse_clustal(REAL)
self.assertEqual(dict(data), {
'abc':
'GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA'
'GUCGAUACGUACGUCAGUCAGUACGUCAGCAUGCAUACGUACGUCGUACGUACGU-CGAC'
'UGACUAGUCAGCUAGCAUCGAUCAGU',
'def':
'------------------------------------------------------------'
'-----------------------------------------CGCGAUGCAUGCAU-CGAU'
'CGAUCAGUCAGUCGAU----------',
'xyz':
'------------------------------------------------------------'
'-------------------------------------CAUGCAUCGUACGUACGCAUGAC'
'UGCUGCAUCA----------------'
})
def test_real(self):
"""Should handle real Clustal output"""
data = parse_clustal(REAL)
self.assertEqual(
dict(data), {
'abc':
'GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA'
'GUCGAUACGUACGUCAGUCAGUACGUCAGCAUGCAUACGUACGUCGUACGUACGU-CGAC'
'UGACUAGUCAGCUAGCAUCGAUCAGU',
'def':
'------------------------------------------------------------'
'-----------------------------------------CGCGAUGCAUGCAU-CGAU'
'CGAUCAGUCAGUCGAU----------',
'xyz':
'------------------------------------------------------------'
'-------------------------------------CAUGCAUCGUACGUACGCAUGAC'
'UGCUGCAUCA----------------'
})
def test_space_labels(self):
"""Should tolerate spaces in labels"""
result = parse_clustal(SPACE_LABELS)
self.assertEqual(dict(result), {'abc': 'uca', 'def ggg': 'ccc'})
def test_two(self):
"""Should handle two-sequence input correctly"""
result = parse_clustal(TWO)
self.assertEqual(dict(result), {'abc': 'uuuaaa', 'def': 'cccggg'})
def test_minimal(self):
"""Should handle single-line input correctly"""
result = parse_clustal([MINIMAL]) # expects seq of lines
self.assertEqual(dict(result), {'abc': 'ucag'})
def test_null(self):
"""Should return empty dict and list on null input"""
result = parse_clustal([])
self.assertEqual(dict(result), {})
def test_space_labels(self):
"""Should tolerate spaces in labels"""
result = parse_clustal(SPACE_LABELS)
self.assertEqual(dict(result), {'abc': 'uca', 'def ggg': 'ccc'})
def test_two(self):
"""Should handle two-sequence input correctly"""
result = parse_clustal(TWO)
self.assertEqual(dict(result), {'abc': 'uuuaaa', 'def': 'cccggg'})
def test_minimal(self):
"""Should handle single-line input correctly"""
result = parse_clustal([MINIMAL]) # expects seq of lines
self.assertEqual(dict(result), {'abc': 'ucag'})
def test_null(self):
"""Should return empty dict and list on null input"""
result = parse_clustal([])
self.assertEqual(dict(result), {})