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_write(self):
"""Should write real Clustal output"""
import os
fname = "test.aln"
testfile = open(fname, 'w')
seqs = [('abc',
'GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA'
'GUCGAUACGUACGUCAGUCAGUACGUCAGCAUGCAUACGUACGUCGUACGUACGU-CGAC'
'UGACUAGUCAGCUAGCAUCGAUCAGU'),
('def',
'------------------------------------------------------------'
'-----------------------------------------CGCGAUGCAUGCAU-CGAU'
'CGAUCAGUCAGUCGAU----------'),
('xyz',
'------------------------------------------------------------'
'-------------------------------------CAUGCAUCGUACGUACGCAUGAC'
'UGCUGCAUCA----------------')]
records = (x for x in seqs)
write_clustal(records, testfile)
testfile.close()
raw = open(fname, 'r').read()
data = parse_clustal(raw.split('\n'))
data = list(data)
self.assertEqual(len(data), len(seqs))
self.assertEqual(set(data), set(seqs))
testfile.close()
os.remove(fname)
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), {})
