def test_get_primers(self): """ Get primer regular expression generators out of mapping data """ # Raise error if ReversePrimer not supplied header = [ 'SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'Description' ] mapping_data = [['s1', 'ATCG', 'TTGGCC,TTGGWC', 'ATRCCTA']] self.assertRaises(IndexError, get_primers, header, mapping_data) header = [ 'SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'ReversePrimer', 'Description' ] forward_primers, reverse_primers = get_primers(header, mapping_data) forward_primers = set([seq.pattern for seq in forward_primers]) reverse_primers = set([seq.pattern for seq in reverse_primers]) expected_forward_primers = set(['TTGGCC', 'TAGG[CT]AT', 'TTGG[AT]C']) expected_reverse_primers = set(['GGCCAA', 'AT[AG]CCTA', 'G[AT]CCAA']) self.assertEqual(forward_primers, expected_forward_primers) self.assertEqual(reverse_primers, expected_reverse_primers)
def test_get_primers(self): """ Get primer regular expression generators out of mapping data """ # Raise error if ReversePrimer not supplied header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'Description'] mapping_data = [['s1', 'ATCG', 'TTGGCC,TTGGWC', 'ATRCCTA']] self.assertRaises(IndexError, get_primers, header, mapping_data) header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'ReversePrimer', 'Description'] forward_primers, reverse_primers = get_primers(header, mapping_data) forward_primers = set([seq.pattern for seq in forward_primers]) reverse_primers = set([seq.pattern for seq in reverse_primers]) expected_forward_primers = set(['TTGGCC', 'TAGG[CT]AT', 'TTGG[AT]C']) expected_reverse_primers = set(['GGCCAA', 'AT[AG]CCTA', 'G[AT]CCAA']) self.assertEqual(forward_primers, expected_forward_primers) self.assertEqual(reverse_primers, expected_reverse_primers)