def __init__(self, settings_module, custom_annotator=None):
self._db = pymongo.MongoClient(host=os.environ.get('MONGO_SERVICE_HOSTNAME', 'localhost'))[settings_module.db_name]
self._population_frequency_store = PopulationFrequencyStore(
db_conn=self._db,
reference_populations=settings_module.reference_populations,
)
self._vep_annotator = HackedVEPAnnotator(
vep_perl_path=settings_module.vep_perl_path,
vep_cache_dir=settings_module.vep_cache_dir,
vep_batch_size=settings_module.vep_batch_size,
human_ancestor_fa=None,
#human_ancestor_fa=settings_module.human_ancestor_fa,
)
self._custom_annotator = custom_annotator
self.reference_populations = settings_module.reference_populations
self.reference_population_slugs = [pop['slug'] for pop in settings_module.reference_populations]
def __init__(self, settings_module, custom_annotator=None):
self._db = pymongo.Connection()[settings_module.db_name]
self._population_frequency_store = PopulationFrequencyStore(
db_conn=self._db,
reference_populations=settings_module.reference_populations,
)
self._vep_annotator = HackedVEPAnnotator(
vep_perl_path=settings_module.vep_perl_path,
vep_cache_dir=settings_module.vep_cache_dir,
vep_batch_size=settings_module.vep_batch_size,
human_ancestor_fa=None,
#human_ancestor_fa=settings_module.human_ancestor_fa,
)
self._custom_annotator = custom_annotator
self.reference_populations = settings_module.reference_populations
self.reference_population_slugs = [
pop['slug'] for pop in settings_module.reference_populations
]
def __init__(self, custom_annotator=None):
self._population_frequency_store = PopulationFrequencyStore(
get_db=self.get_annotator_datastore,
reference_populations=settings.ANNOTATOR_SETTINGS.
reference_populations,
)
self._vep_annotator = HackedVEPAnnotator(
vep_perl_path=settings.ANNOTATOR_SETTINGS.vep_perl_path,
vep_cache_dir=settings.ANNOTATOR_SETTINGS.vep_cache_dir,
vep_batch_size=settings.ANNOTATOR_SETTINGS.vep_batch_size,
human_ancestor_fa=None,
#human_ancestor_fa=settings_module.human_ancestor_fa,
)
self._custom_annotator = custom_annotator
self.reference_populations = settings.ANNOTATOR_SETTINGS.reference_populations
self.reference_population_slugs = [
pop['slug']
for pop in settings.ANNOTATOR_SETTINGS.reference_populations
]
