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)