def genotype(context, force):
"""Upload results from sequencing to the genotype platform."""
mip_case = context.obj["case"]
store = TabooDatabase(context.obj["taboo_db"])
with codecs.open(context.obj["rsnumber_ref"]) as rs_stream:
if mip_case.bcf_path and mip_case.bcf_path.exists():
analyses = load_bcf(store, mip_case.bcf_path, rs_stream, force=force)
else:
analyses = load_vcf(store, mip_case.ready_vcf, rs_stream, force=force)
for analysis in analyses:
logger.info("added analysis: %s", analysis.sample.sample_id)
sample_id = analysis.sample.sample_id
ped_sex = mip_case.ped.individuals[sample_id].sex
analysis.sample.expected_sex = SEX[ped_sex]
store.save()
def parse_payload(db, payload, config, force=False):
"""Process an action to upload genotypes."""
taboo_db = TabooDatabase(config['TABOO_URI'])
mip_analysis = load_analysis(payload['family_dir'])
with open(config['TABOO_RSNUMBERS']) as rs_stream:
if mip_analysis.bcf_path and mip_analysis.bcf_path.exists():
analyses = load_bcf(taboo_db, mip_analysis.bcf_path, rs_stream,
force=force)
else:
analyses = load_vcf(taboo_db, mip_analysis.ready_vcf, rs_stream,
force=force)
for analysis in analyses:
logger.info("added analysis: %s", analysis.sample.sample_id)
sample_id = analysis.sample.sample_id
ped_sex = mip_analysis.ped.individuals[sample_id].sex
analysis.sample.expected_sex = SEX[ped_sex]
taboo_db.save()
def physical_taboodb(temp_folder):
db_path = os.path.join(temp_folder, 'genotype.sqlite3')
db = TabooDatabase(db_path)
db.setup()
return db
def get_dependency(self, worker_ctx):
database = Database(self.uri)
database.reference = self.reference
database.query = database.session.query
self.sessions[worker_ctx] = database.session
return database
