def testSpacesMustBePreserved(self):
"""
If there are spaces in the query title or subject titles, the spaces
must be preserved.
"""
mockOpener = mockOpen(read_data=DIAMOND_RECORD_WITH_SPACES)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
acc94 = list(reader.records())
self.assertEqual('ACC 94', acc94[0]['query'])
self.assertEqual('IN SV', acc94[0]['alignments'][0]['title'])
def testSpacesMustBePreserved(self):
"""
If there are spaces in the query title or subject titles, the spaces
must be preserved.
"""
mockOpener = mockOpen(read_data=DIAMOND_RECORD_WITH_SPACES_IN_TITLES)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
acc94 = list(reader.records())
self.assertEqual('ACC 94', acc94[0]['query'])
self.assertEqual('IN SV', acc94[0]['alignments'][0]['title'])
def testDiamondInput(self):
"""
Test conversion of a chunk of DIAMOND output.
"""
mockOpener = mockOpen(read_data=DIAMOND_RECORDS)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
acc94, akav, bhav = list(reader.records())
self.assertEqual(5, len(acc94['alignments']))
self.assertEqual(2, len(akav['alignments']))
self.assertEqual(2, len(bhav['alignments']))
def testDiamondInput(self):
"""
Test conversion of a chunk of DIAMOND output.
"""
mockOpener = mockOpen(read_data=DIAMOND_RECORDS)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
acc94, akav, bhav = list(reader.records())
self.assertEqual(5, len(acc94['alignments']))
self.assertEqual(2, len(akav['alignments']))
self.assertEqual(2, len(bhav['alignments']))
def testDiamondInputWithoutNidentOrPositives(self):
"""
Test conversion of a chunk of DIAMOND output that does not contain the
nident or positives fields.
"""
mockOpener = mockOpen(
read_data=DIAMOND_RECORDS_WITHOUT_NIDENT_AND_POSITIVE)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
acc94, akav, bhav = list(reader.records())
for record in acc94, akav, bhav:
for alignment in record['alignments']:
for hsp in alignment['hsps']:
self.assertIs(None, hsp['identicalCount'])
def testDiamondInputWithoutNidentOrPositives(self):
"""
Test conversion of a chunk of DIAMOND output that does not contain the
nident or positives fields.
"""
mockOpener = mockOpen(
read_data=DIAMOND_RECORDS_WITHOUT_NIDENT_AND_POSITIVE)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
acc94, akav, bhav = list(reader.records())
for record in acc94, akav, bhav:
for alignment in record['alignments']:
for hsp in alignment['hsps']:
self.assertIs(None, hsp['identicalCount'])
def testDiamondParams(self):
"""
When a DIAMOND file has been read, its parameters must be present
in the reader instance.
"""
mockOpener = mockOpen(read_data=DIAMOND_RECORDS)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
list(reader.records())
self.assertEqual('DIAMOND', reader.application)
self.assertEqual(
{
'application': 'DIAMOND',
'reference': (
'Buchfink et al., Fast and Sensitive Protein '
'Alignment using DIAMOND, Nature Methods, 12, '
'59-60 (2015)'),
'task': 'blastx',
'version': 'v0.8.23',
},
reader.params)
def testDiamondParams(self):
"""
When a DIAMOND file has been read, its parameters must be present
in the reader instance.
"""
mockOpener = mockOpen(read_data=DIAMOND_RECORDS)
with patch.object(builtins, 'open', mockOpener):
reader = DiamondTabularFormatReader('file.txt')
list(reader.records())
self.assertEqual('DIAMOND', reader.application)
self.assertEqual(
{
'application':
'DIAMOND',
'reference':
('Buchfink et al., Fast and Sensitive Protein '
'Alignment using DIAMOND, Nature Methods, 12, '
'59-60 (2015)'),
'task':
'blastx',
'version':
'v0.8.23',
}, reader.params)