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))