def test_get_transcript_expression_levels(self, _get_feature_ids):
exp_utils = ExpressionUtils(self.__class__.cfg) # no logger specified
fpkm_dict, tpm_dict = exp_utils.get_expression_levels(
filepath='data/expression_utils/t_data.ctab',
genome_ref='',
id_col=5)
print(fpkm_dict, tpm_dict)
expected_fpkm = {
'MSTRG.1.1': 17.276905044091045,
'mRNA_1': 0.0,
'MSTRG.1.2': 15.496161235946962,
'mRNA_3': 0.0,
'MSTRG.2.2': 15.833910686877843,
'mRNA_2': 0.0,
'MSTRG.2.1': 16.618558913364847,
'MSTRG.3.1': 19.127090666492997,
'gene_1_mRNA': 0.0
}
expected_tpm = {
'MSTRG.1.1': 17.37137277377277,
'mRNA_3': 0.0,
'MSTRG.1.2': 15.590627562938757,
'mRNA_1': 0.0,
'MSTRG.2.2': 15.928377426832572,
'mRNA_2': 0.0,
'MSTRG.2.1': 16.713026310072223,
'MSTRG.3.1': 19.22155881227908,
'gene_1_mRNA': 0.0
}
self.assertEqual(fpkm_dict, expected_fpkm)
self.assertEqual(tpm_dict, expected_tpm)
def test_get_expression_levels_stringtie(self):
exp_utils = ExpressionUtils(self.__class__.cfg) # no logger specified
fpkm_dict, tpm_dict = exp_utils.get_expression_levels(
filepath='data/expression_utils/stringtie.genes.fpkm_tracking')
self.assertEquals(49, len(fpkm_dict))
self.assertEquals(49, len(tpm_dict))
def test_bad_run_stringtie_app_params(self, _get_feature_ids):
exp_utils = ExpressionUtils(self.__class__.cfg) # no logger specified
with self.assertRaisesRegexp(ValueError, 'line.*'):
exp_utils.get_expression_levels(
filepath=
'data/expression_utils/missing_gene.genes.fpkm_tracking',
genome_ref='')
def test_get_expression_levels_cufflinks(self):
exp_utils = ExpressionUtils(self.__class__.cfg,
self.__class__.__LOGGER)
fpkm_dict, tpm_dict = exp_utils.get_expression_levels(
filepath='data/expression_utils/cufflinks.genes.fpkm_tracking')
self.assertEquals(45, len(fpkm_dict))
self.assertEquals(45, len(tpm_dict))
def test_get_expression_levels_cufflinks(self, _get_feature_ids):
exp_utils = ExpressionUtils(self.__class__.cfg,
self.__class__.__LOGGER)
fpkm_dict, tpm_dict = exp_utils.get_expression_levels(
filepath='data/expression_utils/cufflinks.genes.fpkm_tracking',
genome_ref='')
self.assertEquals(10, len(fpkm_dict))
self.assertEquals(10, len(tpm_dict))
def test_get_expression_levels_zero_sum_fpkm(self):
exp_utils = ExpressionUtils(self.__class__.cfg) # no logger specified
fpkm_dict, tpm_dict = exp_utils.get_expression_levels(
filepath='data/expression_utils/zero_sum_fpkm.genes.fpkm_tracking')
self.assertEquals(49, len(fpkm_dict))
self.assertEquals(49, len(tpm_dict))
sum_tpm = 0.0
for tpm in tpm_dict.values():
sum_tpm += tpm
self.assertEquals(0.0, sum_tpm)
def setUpClass(cls):
cls.__LOGGER = logging.getLogger('ExpressionUtils_test')
cls.__LOGGER.setLevel(logging.INFO)
streamHandler = logging.StreamHandler(sys.stdout)
formatter = logging.Formatter(
"%(asctime)s - %(filename)s - %(lineno)d - %(levelname)s - %(message)s"
)
formatter.converter = time.gmtime
streamHandler.setFormatter(formatter)
cls.__LOGGER.addHandler(streamHandler)
cls.__LOGGER.info("Logger was set")
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('ExpressionUtils'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({
'token':
token,
'user_id':
user_id,
'provenance': [{
'service': 'ExpressionUtils',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.cfg['SDK_CALLBACK_URL'] = cls.callback_url
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = ExpressionUtils(cls.cfg)
cls.scratch = cls.cfg['scratch']