def test_different_format(self, tmpdir, filetype, combined_output_type,
which_names, extant_files, num_cores):
""" File content is actually combined, and formats can differ. """
# Manual creation of the processor here to control output type.
path_output_file = tmpdir.join(
"testfile.{}".format(combined_output_type)).strpath
processor = IdentityProcessor(PATH_ALIGNED_FILE,
cores=num_cores,
outfile=path_output_file,
intermediate_output_type=filetype)
processor.temp_folder = tmpdir.strpath
# Write to the dummy output file for each chunk.
expected_lines = {
fp: "file{}: {}\n".format(i, fp)
for i, fp in enumerate(extant_files)
}
for fp, line in expected_lines.items():
with open(fp, 'w') as f:
f.write(line)
# For control, enforce that combined output doesn't already exist.
assert not os.path.exists(path_output_file)
processor.combine(self.CHUNK_NAMES[which_names], strict=True)
assert os.path.isfile(path_output_file)
# Check that output was combined accurately.
with open(path_output_file, 'r') as combined:
observed_lines = combined.readlines()
assert set(expected_lines.values()) == set(observed_lines)
def test_nothing_to_combine(self, tmpdir, path_logs_file, num_cores,
error_if_missing):
""" Complete lack of output is sufficient to warrant a warning. """
# Create the processor and do combine() step.
path_output_file = tmpdir.join("output.txt").strpath
processor = IdentityProcessor(PATH_ALIGNED_FILE,
cores=num_cores,
outfile=path_output_file)
num_logs_before_combine = len(loglines(path_logs_file))
processor.combine(good_chromosomes=[], strict=error_if_missing)
log_records = loglines(path_logs_file)
# The log record should be a warning, and there's only one.
assert 1 == len(log_records) - num_logs_before_combine
assert "WARN" in log_records[num_logs_before_combine]