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)