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