def test_parse_reads_with_single_read_file_returns_correct_events(
single_read_test_file, single_read_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(single_read_test_file))
for i, event in enumerate(reads[0].events):
expected_event = single_read_expected["events"][i]
assert is_event_correct(event, expected_event) == True
def test_parse_reads_with_repeated_kmer_returns_separate_events(
repeated_kmer_test_file, repeated_kmer_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(repeated_kmer_test_file))
for i, event in enumerate(reads[0].events):
expected_event = repeated_kmer_expected["events"][i]
assert is_event_correct(event, expected_event) == True
def test_parse_reads_with_model_kmer_NNNNN_returns_correct_events(
model_kmer_NNNNN_test_file, model_kmer_NNNNN_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(model_kmer_NNNNN_test_file))
for i, _ in enumerate(reads):
for j, event in enumerate(reads[i].events):
expected_event = model_kmer_NNNNN_expected[i]["events"][j]
assert is_event_correct(event, expected_event) == True
def test_parse_reads_with_skipped_position_returns_correct_events(
skipped_position_test_file, skipped_position_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(skipped_position_test_file))
for i, _ in enumerate(reads):
for j, event in enumerate(reads[i].events):
expected_event = skipped_position_expected[i]["events"][j]
assert is_event_correct(event, expected_event) == True
def test_parse_reads_with_repeated_position_returns_correct_indexes(
repeated_position_test_file, repeated_position_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(repeated_position_test_file))
for i, event in enumerate(reads[0].events):
expected_event = repeated_position_expected["events"][i]
assert event.start_idx == expected_event["start_idx"]
assert event.end_idx == expected_event["end_idx"]
def test_parse_writes_reads_to_h5_file_with_event_order_preserved():
parser = AlignedEventParser(EventalignReadParser())
parser.parse("{0}position_ordering.tsv".format(IN), OUT)
expected_events = [
"event-10", "event-11", "event-12", "event-101", "event-102",
"event-103"
]
actual_events = []
with h5py.File("{0}position_ordering.h5".format(OUT), "r") as h5:
read = h5["read-c1654154-560c-42e4-a8c1-197e9ade83fb"]
for event in read:
actual_events.append(event)
assert actual_events == expected_events
def test_parse_writes_reads_to_h5_file():
parser = AlignedEventParser(EventalignReadParser())
parser.parse("{0}multiple_reads.tsv".format(IN), OUT)
expected_reads = {
"read-c1654154-560c-42e4-a8c1-197e9ade83fb",
"read-8c329395-b3c6-41f2-82a8-b2b78b4c19de",
"read-fb90c5fa-859e-455a-87d4-cac02fa565e7"
}
actual_reads = set()
with h5py.File("{0}multiple_reads.h5".format(OUT), "r") as h5:
for read in h5.keys():
actual_reads.add(read)
assert actual_reads == expected_reads
def test_parse_reads_with_multiple_read_file_returns_correct_contigs(
multiple_read_test_file, multiple_read_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(multiple_read_test_file))
for i, read in enumerate(reads):
assert read.contig == multiple_read_expected[i]["contig"]
def test_parse_reads_with_multiple_read_file_returns_multiple_reads(
multiple_read_test_file, multiple_read_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(multiple_read_test_file))
assert len(reads) == len(multiple_read_expected)
def test_parse_reads_with_single_read_file_returns_correct_contig(
single_read_test_file, single_read_expected):
parser = EventalignReadParser()
reads = list(parser.parse_reads(single_read_test_file))
assert reads[0].contig == single_read_expected["contig"]
def test_parse_reads_with_single_read_file_returns_one_read(
single_read_test_file):
parser = EventalignReadParser()
reads = list(parser.parse_reads(single_read_test_file))
assert len(reads) == 1
def test_parse_raises_exception_if_file_not_found():
parser = AlignedEventParser(EventalignReadParser())
with pytest.raises(FileNotFoundError):
parser.parse("{0}fake_file.tsv".format(IN), OUT)
def test_parse_writes_h5_file_with_correct_path():
parser = AlignedEventParser(EventalignReadParser())
parser.parse("{0}model_kmer_NNNNN.tsv".format(IN), OUT)
assert os.path.isfile('{0}model_kmer_NNNNN.h5'.format(OUT)) == True