def test_humann2_rna_dna_norm_log_10_tsv(self):
"""
Test norm the tsv file entries from dna and rna input files with humann2_rna_dna_norm_table
Test with log transform with base 10
"""
# create a temp folder
tempdir = utils.create_temp_folder("rna_dna_norm_log_10")
output_basename = os.path.join(tempdir, "rna_dna_norm")
# run the command
utils.run_command([
"humann2_rna_dna_norm", "--input_dna", cfg.rna_dna_norm_dna_input,
"--input_rna", cfg.rna_dna_norm_rna_input, "--output_basename",
output_basename, "--log_transform", "--log_base", "10"
])
# check the output files are as expected
# allow for varying precision in the calculations with almost equal
for file_extension, expected_output_file in zip(
cfg.rna_dna_norm_file_names,
cfg.rna_dna_norm_log_10_output_files):
self.assertTrue(
utils.files_almost_equal(output_basename + file_extension,
expected_output_file))
# remove the temp file
utils.remove_temp_folder(tempdir)
def test_humann2_rna_dna_norm_witten_bell_tsv(self):
"""
Test norm the tsv file entries from dna and rna input files with humann2_rna_dna_norm_table
Test with witten bell
"""
# create a temp folder
tempdir = utils.create_temp_folder("rna_dna_norm_witten_bell")
output_basename = os.path.join(tempdir, "rna_dna_norm")
# run the command
utils.run_command([
"humann2_rna_dna_norm", "--input_dna", cfg.rna_dna_norm_dna_input,
"--input_rna", cfg.rna_dna_norm_rna_input, "--output_basename",
output_basename, "--method", "witten_bell"
])
# check the output files are as expected
for file_extension, expected_output_file in zip(
cfg.rna_dna_norm_file_names,
cfg.rna_dna_norm_witten_bell_output_files):
self.assertTrue(
utils.files_almost_equal(output_basename + file_extension,
expected_output_file))
# remove the temp file
utils.remove_temp_folder(tempdir)
def _save_resource(logger, resource, resource_path, target_path):
if not target_path:
target_path = os.path.join(utils.create_temp_folder(), os.path.basename(resource_path))
with open(target_path, "w") as f:
f.write(resource)
logger.info("Downloaded %s to %s" % (resource_path, target_path))
return target_path
def test_humann_fastq_biom_output(self):
"""
Test the standard humann flow on a fastq input file
Test biom output is written
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("fastq")
# run humann test
command = ["humann","--input",cfg.demo_fastq,"--output",tempdir,
"--output-format", "biom"]
utils.run_humann(command)
# check the output files are as expected
for expression, message in utils.check_output(cfg.expected_demo_output_files_biom, tempdir):
self.assertTrue(expression,message)
# remove the temp directory
utils.remove_temp_folder(tempdir)
def test_humann2_fastq_bypass_translated_search(self):
"""
Test the standard humann2 flow on a fastq input file
Test with bypassing translated search
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("fastq_bypass_translated_search")
# run humann2 test
command = [
"humann2", "--input", cfg.demo_fastq, "--output", tempdir,
"--bypass-translated-search"
]
utils.run_humann2(command)
# check the output files are as expected
for expression, message in utils.check_output(
cfg.expected_demo_output_files, tempdir):
self.assertTrue(expression, message)
# remove the temp directory
utils.remove_temp_folder(tempdir)
def test_humann2_strain_profile_tsv(self):
"""
Test the tsv file entries running humann2_strain_profile
Test with critical mean and critical count values
"""
# create a temp folder
tempdir = utils.create_temp_folder("strain_profile")
# move to this folder as the output files will be created in the current working folder
current_working_directory = os.getcwd()
try:
os.chdir(tempdir)
except EnvironmentError:
print("Warning: Unable to move to temp directory: " + tempdir)
# run the command
utils.run_command([
"humann2_strain_profiler", "--input", cfg.strain_profile_input,
"--critical_mean", "1", "--critical_count", "2"
])
# check the output files are as expected
# allow for varying precision in the calculations with almost equal
for file, expected_output_file in zip(
cfg.strain_profile_file_names,
cfg.strain_profile_m1_n2_output_files):
self.assertTrue(
utils.files_almost_equal(os.path.join(tempdir, file),
expected_output_file))
# return to original working directory
os.chdir(current_working_directory)
# remove the temp file
utils.remove_temp_folder(tempdir)
