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 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)
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')
def setUp(self): reference_db = pymongo.MongoClient()['xbrowse_reference'] self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******") annotator_db = pymongo.MongoClient()['xbrowse_annotator'] self.annotator = VariantAnnotator(annotator_db, self.reference) self.populations = ['g1k_all', 'esp_ea', 'esp_aa', 'atgu_controls']
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)
class InternalLookupsTests(unittest.TestCase): """ Test the different internal methods that query ensembl db and rest api """ def setUp(self): reference_db = pymongo.Connection().xbrowse_reference self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******") def test_phenotype_info(self): p = self.reference._get_ensembl_phenotype_info('ENSG00000196218') self.assertEqual(p['mim_id'], '180901') self.assertEqual(len(p['mim_phenotypes']), 4) self.assertEqual(len(p['orphanet_phenotypes']), 7)
class InternalLookupsTests(unittest.TestCase): """ Test the different internal methods that query ensembl db and rest api """ def setUp(self): reference_db = pymongo.MongoClient()['xbrowse_reference'] self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******") def test_phenotype_info(self): p = self.reference._get_ensembl_phenotype_info('ENSG00000196218') self.assertEqual(p['mim_id'], '180901') self.assertEqual(len(p['mim_phenotypes']), 4) self.assertEqual(len(p['orphanet_phenotypes']), 7)
def setUp(self): reference_db = pymongo.Connection().xbrowse_reference self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******")
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 setUp(self): reference_db = pymongo.Connection().xbrowse_reference self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******")
import os os.environ['DJANGO_SETTINGS_MODULE'] = 'settings' import django django.setup() import pymongo from xbrowse.reference import Reference from xbrowse.annotation import VariantAnnotator from xbrowse.coverage import CoverageDatastore from xbrowse.datastore import MongoDatastore import reference_settings import annotator_settings from xbrowse_server.base.models import Project, Family, Individual reference_db = pymongo.MongoClient('xbrowse_reference') reference = Reference(reference_settings) annotator_db = pymongo.MongoClient('xbrowse_annotator') annotator = VariantAnnotator(annotator_settings, reference) annotator._ensure_indices() datastore_db = pymongo.MongoClient('xbrowse_datastore') datastore = MongoDatastore(datastore_db, annotator) user_ns = { 'annotator': annotator, 'datastore': datastore, 'Project': Project, 'Family': Family, 'Individual': Individual, }
def setUp(self): reference_db = pymongo.MongoClient()['xbrowse_reference'] self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******")
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)
#!/usr/bin/env python import pymongo from xbrowse.reference import Reference from xbrowse.annotation import VariantAnnotator from xbrowse.coverage import CoverageDatastore from xbrowse.datastore import MongoDatastore reference_db = pymongo.Connection()['xbrowse_reference'] reference = Reference(reference_db, ensembl_db_host='useastdb.ensembl.org', ensembl_db_user="******") annotator_db = pymongo.Connection()['xbrowse_annotator'] annotator = VariantAnnotator(annotator_db, reference) annotator._ensure_indices() coverage_db = pymongo.Connection()['xbrowse_coverage'] coverage_store = CoverageDatastore(coverage_db, reference) datastore_db = pymongo.Connection()['xbrowse_datastore'] datastore = MongoDatastore(datastore_db, annotator) user_ns = { 'reference': reference, 'annotator': annotator, 'coverage_store': coverage_store, 'datastore': datastore, }
# data files REFERENCEDATA_DIR = '/home/vagrant/server_files/' HGMD_OMIM_FILE = REFERENCEDATA_DIR + 'hgmd_omim_genes.txt' REFSEQ_DESCRIPTION_FILE = REFERENCEDATA_DIR + "refseq_descriptions.txt" ESP_TARGET_FILE = REFERENCEDATA_DIR + 'esp_target.interval_list' # # xbrowse stuff # SETTINGS_DIR = '/opt/xbrowse/' reference_settings = imp.load_source('reference_settings', SETTINGS_DIR + 'reference_settings.py') REFERENCE = Reference(reference_settings) population_frequency_store_settings = imp.load_source( 'popfreq_store_settings', SETTINGS_DIR + 'popfreq_store_settings.py') POPULATION_FREQUENCY_STORE = PopulationFrequencyStore( population_frequency_store_settings) vep_settings = imp.load_source('vep_settings', SETTINGS_DIR + 'vep_settings.py') VEP_ANNOTATOR = HackedVEPAnnotator(vep_settings) annotator_settings = imp.load_source('annotator_settings', SETTINGS_DIR + 'annotator_settings.py') ANNOTATOR = VariantAnnotator( settings_module=annotator_settings, reference=REFERENCE,
def get_reference(): global _reference if _reference is None: _reference = Reference(settings.REFERENCE_SETTINGS) return _reference
def setUp(self): reference_db = pymongo.MongoClient()['xbrowse_reference'] self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******")