class Tests(unittest.TestCase): def setUp(self): self.output_directory_path = os.path.join(my_path, 'test-oligotyping-illumina-25K') self.oligotyping = Oligotyping() self.oligotyping.alignment = os.path.join(my_path, 'files/unaligned-25K-illumina-test.fa') self.oligotyping.entropy = os.path.join(my_path, 'files/unaligned-25K-illumina-test-entropy.txt') self.oligotyping.number_of_auto_components = 20 self.oligotyping.min_percent_abundance = 1 self.oligotyping.min_actual_abundance = 100 self.oligotyping.min_number_of_samples = 1 self.oligotyping.min_substantive_abundance = 0 self.oligotyping.project = 'Unaligned 25K Illumina Test' self.oligotyping.quick = True self.oligotyping.generate_sets = False self.oligotyping.cosine_similarity_threshold = 0.5 self.oligotyping.output_directory = self.output_directory_path self.oligotyping.no_display = True self.oligotyping.progress.verbose = False self.oligotyping.run.verbose = False def tearDown(self): pass def test_01_PrefixGenerator(self): prefix = self.oligotyping.get_prefix() self.assertTrue(prefix == 'c20-s1-a1.0-A100-M0') def test_02_Oligotyping(self): self.oligotyping.run_all() def test_03_EnvironmentFile(self): self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-ENVIRONMENT.txt'), os.path.join(self.output_directory_path, 'ENVIRONMENT.txt'))) def test_04_MatrixPercentFile(self): self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-MATRIX-PERCENT.txt'), os.path.join(self.output_directory_path, 'MATRIX-PERCENT.txt'))) def test_05_MatrixCountFile(self): self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-MATRIX-COUNT.txt'), os.path.join(self.output_directory_path, 'MATRIX-COUNT.txt'))) #def test_06_OligotypeSets(self): # self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-OLIGOTYPE-SETS.txt'), # os.path.join(self.output_directory_path, 'OLIGOTYPE-SETS.txt'))) # #def test_07_OligotypesAcrossSamplesMaxNorm(self): # self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-OLIGOS-ACROSS-DATASETS-MAX-NORM.txt'), # os.path.join(self.output_directory_path, 'OLIGOS-ACROSS-DATASETS-MAX-NORM.txt'))) #def test_08_OligotypesAcrossSamplesSumNorm(self): # self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-OLIGOS-ACROSS-DATASETS-SUM-NORM.txt'), # os.path.join(self.output_directory_path, 'OLIGOS-ACROSS-DATASETS-SUM-NORM.txt'))) def test_99_CleanUp(self): shutil.rmtree(self.output_directory_path)
def setUp(self): self.output_directory_path = os.path.join( my_path, 'test-oligotyping-illumina-25K') self.oligotyping = Oligotyping() self.oligotyping.alignment = os.path.join( my_path, 'files/unaligned-25K-illumina-test.fa') self.oligotyping.entropy = os.path.join( my_path, 'files/unaligned-25K-illumina-test-entropy.txt') self.oligotyping.number_of_auto_components = 20 self.oligotyping.min_percent_abundance = 1 self.oligotyping.min_actual_abundance = 100 self.oligotyping.min_number_of_samples = 1 self.oligotyping.project = 'Unaligned 25K Illumina Test' self.oligotyping.quick = True self.oligotyping.generate_sets = True self.oligotyping.cosine_similarity_threshold = 0.5 self.oligotyping.output_directory = self.output_directory_path self.oligotyping.no_display = True self.oligotyping.progress.verbose = False self.oligotyping.run.verbose = False
def setUp(self): self.output_directory_path = os.path.join(my_path, 'test-oligotyping-illumina-25K') self.oligotyping = Oligotyping() self.oligotyping.alignment = os.path.join(my_path, 'files/unaligned-25K-illumina-test.fa') self.oligotyping.entropy = os.path.join(my_path, 'files/unaligned-25K-illumina-test-entropy.txt') self.oligotyping.number_of_auto_components = 20 self.oligotyping.min_percent_abundance = 1 self.oligotyping.min_actual_abundance = 100 self.oligotyping.min_number_of_samples = 1 self.oligotyping.project = 'Unaligned 25K Illumina Test' self.oligotyping.quick = True self.oligotyping.generate_sets = True self.oligotyping.cosine_similarity_threshold = 0.5 self.oligotyping.output_directory = self.output_directory_path self.oligotyping.no_display = True self.oligotyping.progress.verbose = False self.oligotyping.run.verbose = False
class Tests(unittest.TestCase): def setUp(self): self.output_directory_path = os.path.join( my_path, 'test-oligotyping-illumina-25K') self.oligotyping = Oligotyping() self.oligotyping.alignment = os.path.join( my_path, 'files/unaligned-25K-illumina-test.fa') self.oligotyping.entropy = os.path.join( my_path, 'files/unaligned-25K-illumina-test-entropy.txt') self.oligotyping.number_of_auto_components = 20 self.oligotyping.min_percent_abundance = 1 self.oligotyping.min_actual_abundance = 100 self.oligotyping.min_number_of_samples = 1 self.oligotyping.min_substantive_abundance = 0 self.oligotyping.project = 'Unaligned 25K Illumina Test' self.oligotyping.quick = True self.oligotyping.generate_sets = False self.oligotyping.cosine_similarity_threshold = 0.5 self.oligotyping.output_directory = self.output_directory_path self.oligotyping.no_display = True self.oligotyping.progress.verbose = False self.oligotyping.run.verbose = False def tearDown(self): pass def test_01_PrefixGenerator(self): prefix = self.oligotyping.get_prefix() self.assertTrue(prefix == 'c20-s1-a1.0-A100-M0') def test_02_Oligotyping(self): self.oligotyping.run_all() def test_03_EnvironmentFile(self): self.assertTrue( files_are_the_same( os.path.join(my_path, 'files/unaligned-25K-illumina-ENVIRONMENT.txt'), os.path.join(self.output_directory_path, 'ENVIRONMENT.txt'))) def test_04_MatrixPercentFile(self): self.assertTrue( files_are_the_same( os.path.join( my_path, 'files/unaligned-25K-illumina-MATRIX-PERCENT.txt'), os.path.join(self.output_directory_path, 'MATRIX-PERCENT.txt'))) def test_05_MatrixCountFile(self): self.assertTrue( files_are_the_same( os.path.join(my_path, 'files/unaligned-25K-illumina-MATRIX-COUNT.txt'), os.path.join(self.output_directory_path, 'MATRIX-COUNT.txt'))) #def test_06_OligotypeSets(self): # self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-OLIGOTYPE-SETS.txt'), # os.path.join(self.output_directory_path, 'OLIGOTYPE-SETS.txt'))) # #def test_07_OligotypesAcrossSamplesMaxNorm(self): # self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-OLIGOS-ACROSS-DATASETS-MAX-NORM.txt'), # os.path.join(self.output_directory_path, 'OLIGOS-ACROSS-DATASETS-MAX-NORM.txt'))) #def test_08_OligotypesAcrossSamplesSumNorm(self): # self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/unaligned-25K-illumina-OLIGOS-ACROSS-DATASETS-SUM-NORM.txt'), # os.path.join(self.output_directory_path, 'OLIGOS-ACROSS-DATASETS-SUM-NORM.txt'))) def test_99_CleanUp(self): shutil.rmtree(self.output_directory_path)