def test_load_one_file_04(insert_sequences_batch, info):
"""Load single end sequences from a file into the atram database."""
cxn, args = set_up()
db.BATCH_SIZE = 5
file_1 = join('tests', 'data', 'load_seq1.txt')
core_preprocessor.load_one_file(
args, cxn, file_1, 'single_ends', '')
msg = 'Loading "{}" into sqlite database'.format(file_1)
info.assert_called_once_with(msg)
calls = [
call(cxn, [
('seq1', '', 'AAAAAAAAAA'),
('seq2', '', 'AAAAAAAAAAGGGGGGGGGG'),
('seq3', '', 'AAAAAAAAAA'),
('seq4', '', 'AAAAAAAAAA'),
('seq5/3', '', 'AAAAAAAAAAGGGGGGGGGG')]),
call(cxn, [
('seq1', '', 'AAAAAAAAAA'),
('seq2', '', 'AAAAAAAAAAGGGGGGGGGG'),
('seq3', '', 'AAAAAAAAAA'),
('seq4', '', 'AAAAAAAAAAGGGGGGGGGG')])]
insert_sequences_batch.assert_has_calls(calls)
def test_load_one_file_05(insert_sequences_batch, info):
"""Load single end sequences from a file into the atram database."""
cxn, args = set_up()
db.BATCH_SIZE = 5
file_1 = join('tests', 'data', 'load_seq2.txt')
core_preprocessor.load_one_file(args, cxn, file_1, 'mixed_ends')
msg = 'Loading "{}" into sqlite database'.format(file_1)
info.assert_called_once_with(msg)
calls = [
call(cxn, [
('seq6', '1', 'TTTTTTTTTT'),
('seq7', '1', 'TTTTTTTTTTCCCCCCCCCC'),
('seq8/a', '1', 'TTTTTTTTTT'),
('seq8', '2', 'TTTTTTTTTTCCCCCCCCCC')])]
insert_sequences_batch.assert_has_calls(calls)
def test_load_one_file_05(insert_sequences_batch, info):
"""Load single end sequences from a file into the atram database."""
cxn, args = set_up()
db.BATCH_SIZE = 5
file_1 = join('tests', 'data', 'load_seq2.txt')
core_preprocessor.load_one_file(args, cxn, file_1, 'mixed_ends')
msg = 'Loading "{}" into sqlite database'.format(file_1)
info.assert_called_once_with(msg)
calls = [
call(cxn, [('seq6', '1', 'TTTTTTTTTT'),
('seq7', '1', 'TTTTTTTTTTCCCCCCCCCC'),
('seq8/a', '1', 'TTTTTTTTTT'),
('seq8', '2', 'TTTTTTTTTTCCCCCCCCCC')])
]
insert_sequences_batch.assert_has_calls(calls)
def test_load_one_file_02(insert_sequences_batch, info):
"""Load end 1 sequences from a file into the atram database."""
cxn, args = set_up()
db.BATCH_SIZE = 5
file_1 = join('tests', 'data', 'load_seq1.txt')
core_preprocessor.load_one_file(args, cxn, file_1, 'end_1', '1')
msg = 'Loading "{}" into sqlite database'.format(file_1)
info.assert_called_once_with(msg)
calls = [
call(cxn, [('seq1', '1', 'AAAAAAAAAA'),
('seq2', '1', 'AAAAAAAAAAGGGGGGGGGG'),
('seq3', '1', 'AAAAAAAAAA'), ('seq4', '1', 'AAAAAAAAAA'),
('seq5/3', '1', 'AAAAAAAAAAGGGGGGGGGG')]),
call(cxn, [('seq1', '1', 'AAAAAAAAAA'),
('seq2', '1', 'AAAAAAAAAAGGGGGGGGGG'),
('seq3', '1', 'AAAAAAAAAA'),
('seq4', '1', 'AAAAAAAAAAGGGGGGGGGG')])
]
insert_sequences_batch.assert_has_calls(calls)
