def test_humann2_gene_families_biom_input(self):
"""
Test the standard humann2 flow on a gene families output file as input
Test with the biom format of the gene families file
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("gene_families")
# run humann2 test
command = [
"humann2", "--input", cfg.demo_gene_families_biom, "--output",
tempdir
]
utils.run_humann2(command)
# check the output files are as expected
# it will include all output files except the gene families output file
# since this file was used as input
for expression, message in utils.check_output(
cfg.expected_demo_output_files_genefamilies_input, tempdir):
self.assertTrue(expression, message)
# remove the temp directory
utils.remove_temp_folder(tempdir)
def test_humann2_fastq_biom_output_pathways(self):
"""
Test the standard humann2 flow on a fastq input file
Test biom output is written
Test the expected pathways are identified
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("fastq")
# run humann2 test
command = [
"humann2", "--input", cfg.demo_fastq, "--output", tempdir,
"--output-format", "biom", "--gap-fill", "off"
]
utils.run_humann2(command)
# check the output file of pathway abundance has the expected pathways
pathways_file_tsv = utils.read_biom_table(
os.path.join(tempdir, "demo_pathabundance.biom"))
pathways_found = set([
x.split("\t")[0].split(":")[0]
for x in filter(lambda x: "PWY" in x, pathways_file_tsv)
])
self.assertEqual(pathways_found,
cfg.expected_demo_output_files_biom_pathways)
# remove the temp directory
utils.remove_temp_folder(tempdir)
def test_humann2_m8(self):
"""
Test the standard humann2 flow on a m8 input file
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("m8")
# run humann2 test
command = ["humann2", "--input", cfg.demo_m8, "--output", tempdir]
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_fastq_biom_output(self):
"""
Test the standard humann2 flow on a fastq input file
Test biom output is written
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("fastq")
# run humann2 test
command = [
"humann2", "--input", cfg.demo_fastq, "--output", tempdir,
"--output-format", "biom"
]
utils.run_humann2(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_custom_taxonomic_profile(self):
"""
Test the standard humann2 flow on a fastq input file
Test with a custom taxonomic profile
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("fastq_custom_taxonomic_profile")
# run humann2 test
command = [
"humann2", "--input", cfg.demo_fastq, "--output", tempdir,
"--taxonomic-profile", cfg.demo_bugs_list
]
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_fasta_bypass_prescreen(self):
"""
Test the standard humann2 flow on a fasta input file
Test with bypassing prescreen
"""
# create a temp directory for output
tempdir = utils.create_temp_folder("fasta_bypass_prescreen")
# run humann2 test
command = [
"humann2", "--input", cfg.demo_fasta, "--output", tempdir,
"--bypass-prescreen"
]
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)
