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']
def setUp(self):
reference_db = pymongo.Connection().xbrowse_reference
self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******")
annotator_db = pymongo.Connection().xbrowse_annotator
self.annotator = VariantAnnotator(annotator_db, self.reference)
self.populations = ['g1k_all', 'esp_ea', 'esp_aa', 'atgu_controls']
def get_annotator():
global _annotator
if _annotator is None:
_annotator = VariantAnnotator(
settings_module=settings.ANNOTATOR_SETTINGS,
custom_annotator=get_custom_annotator(),
)
return _annotator
class AnnotatorTests(unittest.TestCase):
def setUp(self):
reference_db = pymongo.Connection().xbrowse_reference
self.reference = Reference(reference_db, ensembl_db_port=3001, ensembl_db_user="******")
annotator_db = pymongo.Connection().xbrowse_annotator
self.annotator = VariantAnnotator(annotator_db, self.reference)
self.populations = ['g1k_all', 'esp_ea', 'esp_aa', 'atgu_controls']
def test_actn3(self):
annotation = self.annotator.get_annotation_for_variant(11e9+66328095, 'T', 'C', self.populations)
print annotation
def test_103807450(self):
annotation = self.annotator.get_annotation_for_variant(1e9+3807450, 'C', 'A', self.populations)
print annotation
class AnnotatorTests(unittest.TestCase):
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']
def test_actn3(self):
annotation = self.annotator.get_annotation_for_variant(11e9+66328095, 'T', 'C', self.populations)
print annotation
def test_103807450(self):
annotation = self.annotator.get_annotation_for_variant(1e9+3807450, 'C', 'A', self.populations)
print annotation
#!/usr/bin/env python
from xbrowse.reference import Reference
from xbrowse.annotation import VariantAnnotator
from xbrowse.coverage import CoverageDatastore
from xbrowse.datastore import MongoDatastore
import pymongo
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,
}
import IPython
IPython.embed(user_ns=user_ns)
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,
}
import IPython
IPython.embed(user_ns=user_ns)
#!/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,
}
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,
population_frequency_store=POPULATION_FREQUENCY_STORE,
vep_annotator=VEP_ANNOTATOR,
)
_conn = pymongo.Connection()
datastore_db = _conn['xbrowse_datastore']
population_datastore_db = _conn['xbrowse_pop_datastore']
DATASTORE = MongoDatastore(datastore_db, ANNOTATOR)
POPULATION_DATASTORE = PopulationDatastore(population_datastore_db, ANNOTATOR)
coverage_db = _conn['xbrowse_coverage']
COVERAGE_STORE = CoverageDatastore(coverage_db, REFERENCE)
project_datastore_db = _conn['xbrowse_proj_store']
PROJECT_DATASTORE = ProjectDatastore(project_datastore_db, ANNOTATOR)
REFERENCEDATA_DIR = os.path.dirname(os.path.realpath(__file__)) + '/'
HGMD_OMIM_FILE = '/vagrant/xbrowse-laptop-downloads/hgmd_omim_genes.txt'
reference_settings = imp.load_source(
'reference_settings',
os.path.dirname(os.path.realpath(__file__)) + '/reference_settings.py')
REFERENCE = Reference(reference_settings)
CUSTOM_ANNOTATOR = None
annotator_settings = imp.load_source(
'annotator_settings',
os.path.dirname(os.path.realpath(__file__)) + '/annotator_settings.py')
ANNOTATOR = VariantAnnotator(
settings_module=annotator_settings,
custom_annotator=CUSTOM_ANNOTATOR,
)
_conn = pymongo.Connection()
datastore_db = _conn['xbrowse_datastore']
population_datastore_db = _conn['xbrowse_pop_datastore']
# datastore_settings = imp.load_source(
# 'datastore_settings',
# os.path.dirname(os.path.realpath(__file__)) + '/datastore_settings.py'
# )
DATASTORE = MongoDatastore(datastore_db, ANNOTATOR)
POPULATION_DATASTORE = PopulationDatastore(population_datastore_db, ANNOTATOR)
coverage_db = _conn['xbrowse_coverage']
def get_annotator():
global _annotator
if _annotator is None:
_annotator = VariantAnnotator(
custom_annotator=get_custom_annotator(), )
return _annotator
