def testEmpty(self):
"""
An instance of TitlesAlignments must have no titles if passed an
empty readsAlignments instance.
"""
mockOpener = mockOpen(read_data=(PARAMS))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual([], list(titlesAlignments.keys()))
def testEmpty(self):
"""
An instance of TitlesAlignments must have no titles if passed an
empty readsAlignments instance.
"""
mockOpener = mockOpen(read_data=(dumps(PARAMS) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual([], list(titlesAlignments.keys()))
def testEmpty(self):
"""
An instance of TitlesAlignments must have no titles if passed an
empty readsAlignments instance.
"""
mockOpener = mockOpen(read_data=(dumps(PARAMS) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
readsAlignments = DiamondReadsAlignments(reads, 'file.json',
'database.fasta')
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual([], list(titlesAlignments.keys()))
def testExpectedTitles(self):
"""
An instance of TitlesAlignments must have the expected titles.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD0 + RECORD1 + RECORD2))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual(
sorted([
COWPOX.id,
MONKEYPOX.id,
MUMMYPOX.id,
SQUIRRELPOX.id,
CATPOX.id,
]),
sorted(titlesAlignments.keys()))
def testExpectedTitles(self):
"""
An instance of TitlesAlignments must have the expected titles.
"""
mockOpener = mockOpen(
read_data=(dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual([
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
], sorted(titlesAlignments.keys()))
def testExpectedTitles(self):
"""
An instance of TitlesAlignments must have the expected titles.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(titlesAlignments.keys()))
