def test_duplicate_seq_ids(self):
"""Test file with duplicates identifiers."""
file1 = os.path.join(path, "duplicate_names.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1)
assert result_lib_1 == "invalid_file" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
def test_second_mate(self):
"""Test single file, second mate."""
file1 = os.path.join(path, "SRR11971713_2.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1)
assert result_lib_1 == "second_mate" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
def test_single_file(self):
"""Test single file, first mate."""
file_1 = os.path.join(path, "first_mate.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file_1)
assert result_lib_1 == "first_mate" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
def test_compressed_file(self):
"""Test single compressed file."""
file1 = os.path.join(path, "SRR11971558_1.fastq.gz")
result_lib_1, result_lib_2, mate_relationship = infer(file1)
assert result_lib_1 == "mixed_mates" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
def test_max_records():
file1 = os.path.join(path, "first_mate.fastq")
file2 = os.path.join(path, "second_mate.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1, file2, 2)
assert result_lib_1 == "first_mate" and \
result_lib_2 == "second_mate" and \
mate_relationship == "split_mates"
def test_not_mates():
file1 = os.path.join(path, "SRR11972514_1.fastq")
file2 = os.path.join(path, "SRR11971713_2.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1, file2)
assert result_lib_1 == "first_mate" and \
result_lib_2 == "second_mate" and \
mate_relationship == "not_mates"
def test_invalid_identifiers():
file1 = os.path.join(path, "SRR11971713_1.fastq")
file2 = os.path.join(path, "SRR11971558_2.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1, file2)
assert result_lib_1 == "no_mate_info" and \
result_lib_2 == "no_mate_info" and \
mate_relationship == "not_mates"
def test_empty_file(self):
"""Test empty file."""
file1 = os.path.join(path, "SRR11971713_1.fastq")
file1 = os.path.join(path, "empty.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1)
assert result_lib_1 == "invalid_file" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
def test_split_mates(self):
"""Test two files, split mates."""
file1 = os.path.join(path, "first_mate.fastq")
file2 = os.path.join(path, "second_mate.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1, file2)
assert result_lib_1 == "first_mate" and \
result_lib_2 == "second_mate" and \
mate_relationship == "split_mates"
def test_max_records(self):
"""Test two files, split mates; set max records argument"""
file1 = os.path.join(path, "first_mate.fastq")
file2 = os.path.join(path, "second_mate.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(
file_1=file1,
file_2=file2,
max_records=2,
)
assert result_lib_1 == "first_mate" and \
result_lib_2 == "second_mate" and \
mate_relationship == "split_mates"
def main() -> None:
"""Main function.
Args:
args: Command-line arguments and their values.
"""
args = parse_args()
setup_logging(
verbose=args.verbose,
debug=args.debug,
)
logger.info("Started script...")
logger.debug(f"CLI options: {args}")
results = {}
results['single_paired'] = infer_single_paired.infer(
file_1=args.file_1,
file_2=args.file_2,
)
logger.info(f"Results: {results}")
logger.info("Done.")
def test_duplicate_seq_ids():
file1 = os.path.join(path, "duplicate_names.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1)
assert result_lib_1 == "invalid_file" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
def test_invalid_file():
file1 = os.path.join(path, "SRR11972514_1.fast")
result_lib_1, result_lib_2, mate_relationship = infer(file1)
assert result_lib_1 == "invalid_file" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
def test_empty_file():
file1 = os.path.join(path, "empty.fastq")
result_lib_1, result_lib_2, mate_relationship = infer(file1)
assert result_lib_1 == "invalid_file" and \
result_lib_2 == "not_available" and \
mate_relationship == "not_available"
