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()))