def test_humann_m8(self): """ Test the standard humann flow on a m8 input file """ # create a temp directory for output tempdir = utils.create_temp_folder("m8") # run humann test command = ["humann","--input",cfg.demo_m8,"--output",tempdir] utils.run_humann(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_humann_fasta_bypass_prescreen(self): """ Test the standard humann 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 humann test command = ["humann","--input",cfg.demo_fasta,"--output",tempdir,"--bypass-prescreen"] utils.run_humann(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_humann_gene_families(self): """ Test the standard humann flow on a gene families output file as input """ # create a temp directory for output tempdir = utils.create_temp_folder("gene_families") # run humann test command = ["humann","--input",cfg.demo_gene_families,"--output",tempdir] utils.run_humann(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_humann_fastq_custom_taxonomic_profile(self): """ Test the standard humann 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 humann test command = ["humann","--input",cfg.demo_fastq,"--output",tempdir,"--taxonomic-profile", cfg.demo_bugs_list] utils.run_humann(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_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_humann_fastq_biom_output_pathways(self): """ Test the standard humann 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 humann test command = ["humann","--input",cfg.demo_fastq,"--output",tempdir, "--output-format", "biom", "--gap-fill", "off"] utils.run_humann(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)