def test_get_id_from_header_line(self):
'''Test get id from header line of EMBL'''
embl = sequences.Embl('ID', 'ACGT')
self.assertEqual(embl._get_id_from_header_line('ID X; blah'), 'X')
self.assertEqual(embl._get_id_from_header_line('LOCUS X foo'), 'X')
with self.assertRaises(sequences.Error):
self.assertEqual(embl._get_id_from_header_line('ID X;'), 'X')
with self.assertRaises(sequences.Error):
self.assertEqual(embl._get_id_from_header_line('XX X;'), 'X')
def test_get_next_from_embl_file(self):
f_in = utils.open_file_read(os.path.join(data_dir, 'sequences_test.embl'))
embl = sequences.Embl()
counter = 1
while embl.get_next_from_file(f_in):
self.assertEqual(embl, sequences.Fasta('seq' + str(counter), expected_embl[counter-1]))
counter += 1
utils.close(f_in)
def test_get_next_from_gbk_file(self):
f_in = utils.open_file_read(os.path.join(data_dir, 'sequences_test.gbk'))
embl = sequences.Embl()
counter = 1
expected = [
'gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaatgccatgactcagattctaattttaagctattcaatttctctttgatc',
'gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaatgccatgactcagattctaattttaagctattcaatttctctttgaaa']
while embl.get_next_from_file(f_in):
self.assertEqual(embl, sequences.Fasta('NAME' + str(counter), expected[counter-1]))
counter += 1
utils.close(f_in)