def test_humann_split_tables_tsv(self):
"""
Test splitting a tsv file with humann_split_tables
"""
input_file = cfg.multi_sample_genefamilies
# create a temp directory
temp_directory = utils.create_temp_folder("split_tables_tsv")
# split the file
utils.run_command([
"humann_split_table", "--input", input_file, "--output",
temp_directory, "--verbose"
])
# test the split files are as expected
output_files = os.listdir(temp_directory)
# sort the output files
file_pairs = []
for file in output_files:
filebasename = os.path.basename(file)
# get the sample number for the file
file = os.path.join(temp_directory, file)
if filebasename[-1] == 1:
file_pairs.append([file, cfg.multi_sample_genefamilies_split1])
elif filebasename[-1] == 2:
file_pairs.append([file, cfg.multi_sample_genefamilies_split2])
for temp_file, file in file_pairs:
self.assertTrue(utils.files_almost_equal(temp_file, file))
# remove the temp folder
utils.remove_temp_folder(temp_directory)
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_humann_unpack_pathways_remove_taxonomy_tsv(self):
"""
Test the tsv gene families and pathway abundance file entries with humann_unpack_pathways
Test with the remove taxonomy option which stratifies by pathway then gene instead of
stratifying by pathway, taxonomy, then gene
"""
# create a temp file
file_out, new_file = tempfile.mkstemp(prefix="humann_temp")
# run the command
utils.run_command([
"humann_unpack_pathways", "--input-genes",
cfg.merge_abundance_genefamilies_input, "--input-pathways",
cfg.merge_abundance_pathways_input, "--output", new_file,
"--remove-taxonomy"
])
# check the output file is as expected
# allow for varying precision in the calculations with almost equal
self.assertTrue(
utils.files_almost_equal(
new_file, cfg.merge_abundance_remove_taxonomy_output))
# remove the temp file
utils.remove_temp_file(new_file)
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 test_humann_regroup_table_uniref50_rxn_tsv(self):
"""
Test regrouping the tsv file with humann_regroup_table
Test with uniref50 to reactions mappings
"""
# create a temp file
file_out, new_file = tempfile.mkstemp(prefix="humann_temp")
# run the command
utils.run_command([
"humann_regroup_table", "--input", cfg.regroup_input, "--output",
new_file, "--groups", "uniref50_rxn"
])
# check the output is as expected
self.assertTrue(
utils.files_almost_equal(new_file, cfg.regroup_rxn_output))
# remove the temp file
utils.remove_temp_file(new_file)
def test_humann_renorm_table_relab_tsv(self):
"""
Test renorm the tsv file entries with humann_renorm_table
Test with relab
"""
# create a temp file
file_out, new_file = tempfile.mkstemp(prefix="humann_temp")
# run the command
utils.run_command([
"humann_renorm_table", "--input", cfg.renorm_input, "--output",
new_file, "--units", "relab"
])
# check the output is as expected
self.assertTrue(
utils.files_almost_equal(new_file, cfg.renorm_relab_output))
# remove the temp file
utils.remove_temp_file(new_file)
def test_humann_rename_table_custom_tsv(self):
"""
Test renaming the tsv file entries with humann_rename_table
Test with custom names file
"""
# create a temp file
file_out, new_file = tempfile.mkstemp(prefix="humann_temp")
# run the command
utils.run_command([
"humann_rename_table", "--input", cfg.rename_input, "--output",
new_file, "--custom", cfg.rename_custom_mapping
])
# check the output is as expected
self.assertTrue(
utils.files_almost_equal(new_file, cfg.rename_custom_output))
# remove the temp file
utils.remove_temp_file(new_file)
def test_humann_rename_table_pathways_tsv(self):
"""
Test renaming the tsv file entries with humann_rename_table
Test with pathways names
"""
# create a temp file
file_out, new_file = tempfile.mkstemp(prefix="humann_temp")
# run the command
utils.run_command([
"humann_rename_table", "--input", cfg.rename_pathway_input,
"--output", new_file, "--names", "metacyc-pwy"
])
# check the output is as expected
self.assertTrue(
utils.files_almost_equal(new_file, cfg.rename_pathway_output))
# remove the temp file
utils.remove_temp_file(new_file)
def test_humann_join_tables_tsv(self):
"""
Test joining tsv files with humann_join_tables
"""
# create a temp file
file_out, new_file = tempfile.mkstemp(prefix="humann_temp")
# join the files
utils.run_command([
"humann_join_tables", "--input", cfg.data_folder, "--output",
new_file, "--file_name",
cfg.multi_sample_genefamilies_split_basename, "--verbose"
])
# check the joined file is as expected
self.assertTrue(
utils.files_almost_equal(new_file, cfg.multi_sample_genefamilies))
# remove the temp file
utils.remove_temp_file(new_file)
def test_humann2_unpack_pathways_tsv(self):
"""
Test the tsv gene families and pathway abundance file entries with humann2_unpack_pathways
"""
# create a temp file
file_out, new_file = tempfile.mkstemp(prefix="humann2_temp")
# run the command
utils.run_command([
"humann2_unpack_pathways", "--input-genes",
cfg.merge_abundance_genefamilies_input, "--input-pathways",
cfg.merge_abundance_pathways_input, "--output", new_file
])
# check the output file is as expected
# allow for varying precision in the calculations with almost equal
self.assertTrue(
utils.files_almost_equal(new_file, cfg.merge_abundance_output))
# remove the temp file
utils.remove_temp_file(new_file)
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)
