def test_querying_transcripts_by_genes(self): """Test that we can get all of the transcripts for a given set of genes. """ datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False) annotator = Annotator() for ds in datasource_list: annotator.addDatasource(ds) # Step 1 get all of the relevant transcripts txs = annotator.retrieve_transcripts_by_genes(["MAPK1", "PIK3CA"]) self.assertTrue(len(txs) > 3)
def test_querying_transcripts_by_genes(self): """Test that we can get all of the transcripts for a given set of genes. """ datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False) annotator = Annotator() for ds in datasource_list: annotator.addDatasource(ds) # Step 1 get all of the relevant transcripts txs = annotator.retrieve_transcripts_by_genes(["MAPK1", "PIK3CA"]) self.assertTrue(len(txs) > 3)
def test_simple_genes_by_gene_annotation(self): """Test web api backend call /gene/ """ # http://www.broadinstitute.org/oncotator/gene/MAPK1/ datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False) annotator = Annotator() for ds in datasource_list: annotator.addDatasource(ds) txs = annotator.retrieve_transcripts_by_genes(["MAPK1"]) self.assertTranscriptsFound(txs) mut_dict = annotator.annotate_genes_given_txs(txs) self.assertTrue(len(mut_dict.keys()) == 1)
def test_simple_genes_by_gene_annotation(self): """Test web api backend call /gene/ """ # http://www.broadinstitute.org/oncotator/gene/MAPK1/ datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False) annotator = Annotator() for ds in datasource_list: annotator.addDatasource(ds) txs = annotator.retrieve_transcripts_by_genes(["MAPK1"]) self.assertTranscriptsFound(txs) mut_dict = annotator.annotate_genes_given_txs(txs) self.assertTrue(len(mut_dict.keys()) == 1)