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="******")
