def test_gapped_translation_with_mixed_codons(self):
seq = 'TCTN--GAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
self.assertRaises(TranslationErrorMixedGappedSeq, seq_record.translate,
table=1)
try:
seq_record.translate(table=1)
except TranslationErrorMixedGappedSeq as e:
self.assertTrue("Gene" in e.__str__())
def test_translate_with_table_at_function_level(self):
seq = 'TCTGAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
expected = 'SEWKTKRP'
self.assertEqual(expected, seq_record.translate(table=1))
seq = 'ACACGTCGACTCCGGCAAGTCCACTACCACAGGA'
seq_record = SeqRecordExpanded(seq, reading_frame=2)
expected = 'HVDSGKSTTTG'
self.assertEqual(expected, seq_record.translate(table=1))
def test_translate(self):
seq = 'TCTGAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1, table=1)
expected = 'SEWKTKRP'
self.assertEqual(expected, seq_record.translate(), 'Using reading_frame=1')
seq = 'TCTGAATGGAA?ACAAAGCGT???'
seq_record = SeqRecordExpanded(seq, reading_frame=1, table=1)
expected = 'SEWXTKRX'
self.assertEqual(expected, seq_record.translate(), 'Using reading_frame=1')
seq = 'ACACGTCGACTCCGGCAAGTCCACTACCACAGGA'
seq_record = SeqRecordExpanded(seq, reading_frame=2, table=1)
expected = 'HVDSGKSTTTG'
self.assertEqual(expected, seq_record.translate(), 'Using reading_frame=2')
def test_gapped_translation(self):
seq = 'TCT---GAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
expected = 'S-EWKTKRP'
self.assertEqual(expected, seq_record.translate(table=1))
