def testHsps(self):
"""
The hsps function must yield all the hsps for all titles in a
TitlesAlignments instance.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD0 + RECORD1 + RECORD2))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
result = list(titlesAlignments.hsps())
self.assertEqual(
sorted([HSP(READ0_SQUIRRELPOX_SCORE),
HSP(READ0_CATPOX_SCORE),
HSP(READ1_MONKEYPOX_SCORE),
HSP(READ1_MONKEYPOX_HSP2_SCORE),
HSP(READ1_MUMMYPOX_SCORE),
HSP(READ2_COWPOX_SCORE)]),
sorted(result))
def testHsps(self):
"""
The hsps function must yield all the hsps for all titles in a
TitlesAlignments instance.
"""
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)
result = list(titlesAlignments.hsps())
self.assertEqual(
sorted([HSP(20), HSP(25), HSP(20), HSP(20), HSP(20)]),
sorted(result))
def testHsps(self):
"""
The hsps function must yield all the hsps for all titles in a
TitlesAlignments instance.
"""
mockOpener = mock_open(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 = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = list(titlesAlignments.hsps())
self.assertEqual(
sorted([HSP(20), HSP(25), HSP(20), HSP(20), HSP(20)]),
sorted(result))
