class RYR1Tests(unittest.TestCase): def setUp(self): reference_db = pymongo.MongoClient()['xbrowse_reference'] self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******") gene_id = self.reference.get_gene_id_from_symbol('RYR1') self.gene = self.reference.get_gene(gene_id) def test_biotype(self): self.assertEqual(self.gene['biotype'], 'protein_coding') def test_description(self): self.assertEqual( self.gene['description'], 'ryanodine receptor 1 (skeletal) [Source:HGNC Symbol;Acc:10483]') def test_symbol(self): self.assertEqual(self.gene['symbol'], 'RYR1') def test_num_transcripts(self): self.assertEqual(len(self.gene['transcripts']), 13) def test_num_exons(self): self.assertEqual(len(self.gene['exons']), 158)
class ReferenceTests(unittest.TestCase): def setUp(self): reference_db = pymongo.Connection().xbrowse_reference self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******") def test_num_genes(self): self.assertEqual(len(self.reference._get_all_gene_ids()), 30585) def test_symbol_lookup(self): self.assertEqual(self.reference.get_gene_id_from_symbol('RYR1'), 'ENSG00000196218') def test_symbol_lookup_lower(self): self.assertEqual(self.reference.get_gene_id_from_symbol('ryr1'), 'ENSG00000196218') def test_id_lookup(self): self.assertEqual(self.reference.get_gene_symbol('ENSG00000196218'), 'RYR1')
class ReferenceTests(unittest.TestCase): def setUp(self): reference_db = pymongo.MongoClient()['xbrowse_reference'] self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******") def test_num_genes(self): self.assertEqual(len(self.reference._get_all_gene_ids()), 30585) def test_symbol_lookup(self): self.assertEqual(self.reference.get_gene_id_from_symbol('RYR1'), 'ENSG00000196218') def test_symbol_lookup_lower(self): self.assertEqual(self.reference.get_gene_id_from_symbol('ryr1'), 'ENSG00000196218') def test_id_lookup(self): self.assertEqual(self.reference.get_gene_symbol('ENSG00000196218'), 'RYR1')
class RYR1Tests(unittest.TestCase): def setUp(self): reference_db = pymongo.Connection().xbrowse_reference self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******") gene_id = self.reference.get_gene_id_from_symbol('RYR1') self.gene = self.reference.get_gene(gene_id) def test_biotype(self): self.assertEqual(self.gene['biotype'], 'protein_coding') def test_description(self): self.assertEqual(self.gene['description'], 'ryanodine receptor 1 (skeletal) [Source:HGNC Symbol;Acc:10483]') def test_symbol(self): self.assertEqual(self.gene['symbol'], 'RYR1') def test_num_transcripts(self): self.assertEqual(len(self.gene['transcripts']), 13) def test_num_exons(self): self.assertEqual(len(self.gene['exons']), 158)