def test_update(self): """ Test if update on sample data is working """ path_data = "tests/ganon/integration/data/" prefix = "test_update" ret = ganon.main( shlex.split("ganon update --db-prefix " + path_data + "sample_bacteria --output-db-prefix " + prefix + " --taxdump-file " + path_data + "mini_nodes.dmp " + path_data + "mini_names.dmp --seq-info-file " + path_data + "virus_acc_len_taxid.txt --input-files " + path_data + "virus_NC_003676.1.fasta.gz " + path_data + "virus_NC_011646.1.fasta.gz " + path_data + "virus_NC_032412.1.fasta.gz " + path_data + "virus_NC_035470.1.fasta.gz")) # check if ran okay self.assertFalse(ret, "ganon update finish with an error") # check if files were created for ext in ["ibf", "map", "tax", "gnn"]: self.assertTrue( Path(prefix + "." + ext).is_file(), "File (" + ext + ") was not created") # TODO check file contents
def test_build(self): """ Test if build on sample data is working """ path_data = "tests/ganon/integration/data/" prefix = "test_build" ret = ganon.main( shlex.split("ganon build --db-prefix " + prefix + " --taxdump-file " + path_data + "mini_nodes.dmp " + path_data + "mini_names.dmp --seq-info-file " + path_data + "bacteria_acc_len_taxid.txt --input-files " + path_data + "bacteria_NC_010333.1.fasta.gz " + path_data + "bacteria_NC_017164.1.fasta.gz " + path_data + "bacteria_NC_017163.1.fasta.gz " + path_data + "bacteria_NC_017543.1.fasta.gz")) # check if ran okay self.assertFalse(ret, "ganon build finish with an error") # check if files were created for ext in ["filter", "map", "bins", "nodes"]: self.assertTrue( Path(prefix + "." + ext).is_file(), "File (" + ext + ") was not created") # TODO check file contents
def test_report(self): """ Test if report on sample data is working """ path_data = "tests/ganon/integration/data/" output_file = "test_report.tre" ret = ganon.main( shlex.split("./ganon report --output-report " + output_file + " --db-prefix " + path_data + "sample_bacteria --rep-file " + path_data + "results.rep --rank all")) # check if ran okay self.assertFalse(ret, "ganon report finish with an error") # check if files were created self.assertTrue( Path(output_file).is_file(), "File (" + output_file + ") was not created")
def test_classify(self): """ Test if classify on sample data is working """ path_data = "tests/ganon/integration/data/" prefix = "test_classify" ret = ganon.main( shlex.split("./ganon classify --output-all --db-prefix " + path_data + "sample_bacteria --single-reads " + path_data + "bacteria.simulated.1.fq -o " + prefix)) # check if ran okay self.assertFalse(ret, "ganon classify finish with an error") # check if files were created for ext in ["lca", "all", "rep", "tre"]: self.assertTrue( Path(prefix + "." + ext).is_file(), "File (" + ext + ") was not created") # TODO check file contents