def load_panel(self, parsed_panel):
"""Load a gene panel based on the info sent
A panel object is built and integrity checks are made.
The panel object is then loaded into the database.
Args:
path(str): Path to panel file
institute(str): Name of institute that owns the panel
panel_id(str): Panel id
date(datetime.datetime): Date of creation
version(float)
full_name(str): Option to have a long name
panel_info(dict): {
'file': <path to panel file>(str),
'institute': <institute>(str),
'type': <panel type>(str),
'date': date,
'version': version,
'panel_name': panel_id,
'full_name': name,
}
"""
panel_obj = build_panel(parsed_panel, self)
self.add_gene_panel(panel_obj)
def load_panel(self, parsed_panel):
"""Load a gene panel based on the info sent
A panel object is built and integrity checks are made.
The panel object is then loaded into the database.
Args:
path(str): Path to panel file
institute(str): Name of institute that owns the panel
panel_id(str): Panel id
date(datetime.datetime): Date of creation
version(float)
full_name(str): Option to have a long name
panel_info(dict): {
'file': <path to panel file>(str),
'institute': <institute>(str),
'type': <panel type>(str),
'date': date,
'version': version,
'panel_name': panel_id,
'full_name': name,
}
"""
panel_obj = build_panel(parsed_panel, self)
self.add_gene_panel(panel_obj)
def load_panel(adapter, panel_info):
"""Load a gene panel into the databse
Args:
adapter(MongoAdapter)
panel_info(dict)
"""
panel_data = parse_gene_panel(panel_info)
panel_obj = build_panel(panel_data, adapter)
# Check if the panel exists in database
panel = adapter.gene_panel(panel_obj['panel_name'], panel_obj['version'])
if not panel:
adapter.add_gene_panel(panel_obj)
else:
logger.info("Panel {} version {} already exists".format(panel_obj['panel_name'],
panel_obj['version']))
def load_panel(self,
path,
institute,
panel_id,
date,
panel_type='clinical',
version=1.0,
display_name=None):
"""Load a gene panel based on the info sent
The panel info is first parsed, then a panel object is built and integrity checks are made.
The panel object is then loaded into the database.
Args:
path(str): Path to panel file
institute(str): Name of institute that owns the panel
panel_id(str): Panel id
date(datetime.datetime): Date of creation
version(float)
full_name(str): Option to have a long name
panel_info(dict): {
'file': <path to panel file>(str),
'institute': <institute>(str),
'type': <panel type>(str),
'date': date,
'version': version,
'panel_name': panel_id,
'full_name': name,
}
"""
panel_data = parse_gene_panel(
path=path,
institute=institute,
panel_type=panel_type,
date=date,
version=version,
panel_id=panel_id,
display_name=display_name,
)
panel_obj = build_panel(panel_data, self)
self.add_gene_panel(panel_obj)
def load_omim_panel(self, genemap2_lines, mim2gene_lines, institute=None):
"""Create and load the OMIM-AUTO panel
If the panel already exists, update with new information and increase version
Args:
genemap_lines(iterable(str)): The genemap2 file information
mim2gene_lines(iterable(str)): The mim2genes file information
institute(str): What institute that is responsible. Default: 'cust002'
"""
institute = institute or "cust002"
existing_panel = self.gene_panel(panel_id="OMIM-AUTO")
if not existing_panel:
LOG.warning("OMIM-AUTO does not exists in database")
LOG.info("Creating a first version")
version = 1.0
if existing_panel:
version = float(math.floor(existing_panel["version"]) + 1)
LOG.info("Setting version to %s", version)
date_string = None
# Get the correct date when omim files where released
for line in genemap2_lines:
if "Generated" in line:
date_string = line.split(":")[-1].strip()
break
date_obj = get_date(date_string)
if existing_panel:
if existing_panel["date"] == date_obj:
LOG.warning("There is no new version of OMIM")
return
panel_data = {
"path": None,
"type": "clinical",
"date": date_obj,
"panel_id": "OMIM-AUTO",
"institute": institute,
"version": version,
"display_name": "OMIM-AUTO",
"genes": [],
}
alias_genes = self.genes_by_alias()
genes = get_omim_panel_genes(
genemap2_lines=genemap2_lines,
mim2gene_lines=mim2gene_lines,
alias_genes=alias_genes,
)
for gene in genes:
panel_data["genes"].append(gene)
panel_obj = build_panel(panel_data, self)
if existing_panel:
new_genes = self.compare_mim_panels(existing_panel, panel_obj)
if not new_genes:
LOG.info("The new version of omim does not differ from the old one")
LOG.info("No update is added")
return
self.update_mim_version(
new_genes, panel_obj, old_version=existing_panel["version"]
)
self.add_gene_panel(panel_obj)
def load_omim_panel(self, api_key, institute=None):
"""Create and load the OMIM-AUTO panel"""
existing_panel = self.gene_panel(panel_id='OMIM-AUTO')
if not existing_panel:
LOG.warning("OMIM-AUTO does not exists in database")
LOG.info('Creating a first version')
version = 1.0
if existing_panel:
version = float(math.floor(existing_panel['version']) + 1)
LOG.info("Setting version to %s", version)
try:
mim_files = fetch_mim_files(api_key=api_key, genemap2=True, mim2genes=True)
except Exception as err:
raise err
date_string = None
# Get the correct date when omim files where released
for line in mim_files['genemap2']:
if 'Generated' in line:
date_string = line.split(':')[-1].lstrip().rstrip()
date_obj = get_date(date_string)
if existing_panel:
if existing_panel['date'] == date_obj:
LOG.warning("There is no new version of OMIM")
return
panel_data = {}
panel_data['path'] = None
panel_data['type'] = 'clinical'
panel_data['date'] = date_obj
panel_data['panel_id'] = 'OMIM-AUTO'
panel_data['institute'] = institute or 'cust002'
panel_data['version'] = version
panel_data['display_name'] = 'OMIM-AUTO'
panel_data['genes'] = []
alias_genes = self.genes_by_alias()
genes = get_omim_panel_genes(
genemap2_lines = mim_files['genemap2'],
mim2gene_lines = mim_files['mim2genes'],
alias_genes = alias_genes,
)
for gene in genes:
panel_data['genes'].append(gene)
panel_obj = build_panel(panel_data, self)
if existing_panel:
new_genes = self.compare_mim_panels(existing_panel, panel_obj)
if new_genes:
self.update_mim_version(new_genes, panel_obj, old_version=existing_panel['version'])
else:
LOG.info("The new version of omim does not differ from the old one")
LOG.info("No update is added")
return
self.add_gene_panel(panel_obj)
def panel_obj(request, parsed_panel, gene_database):
"""docstring for parsed_panels"""
panel = build_panel(parsed_panel, gene_database)
return panel
def panel_obj(request, parsed_panel, gene_database):
"""Return a panel object"""
panel = build_panel(parsed_panel, gene_database)
return panel
def demo(context):
"""Setup a scout demo instance. This instance will be populated with a
case a gene panel and some variants.
"""
log.info("Running scout setup demo")
institute_name = context.obj['institute_name']
user_name = context.obj['user_name']
user_mail = context.obj['user_mail']
adapter = context.obj['adapter']
log.info("Setting up database %s", context.obj['mongodb'])
log.info("Deleting previous database")
for collection_name in adapter.db.collection_names():
log.info("Deleting collection %s", collection_name)
adapter.db.drop_collection(collection_name)
log.info("Database deleted")
# Build a institute with id institute_name
institute_obj = build_institute(
internal_id=institute_name,
display_name=institute_name,
sanger_recipients=[user_mail]
)
# Add the institute to database
adapter.add_institute(institute_obj)
# Build a user obj
user_obj = dict(
_id=user_mail,
email=user_mail,
name=user_name,
roles=['admin'],
institutes=[institute_name]
)
adapter.add_user(user_obj)
# Load the genes and transcripts
hgnc_handle = context.obj['hgnc']
transcripts37_handle = context.obj['transcripts37']
# transcripts38_handle = context.obj['transcripts38']
exac_handle = context.obj['exac']
hpo_genes_handle = context.obj['hpogenes']
mim2gene_handle = context.obj['mim2gene']
genemap_handle = context.obj['genemap2']
genes37 = link_genes(
ensembl_lines=transcripts37_handle,
hgnc_lines=hgnc_handle,
exac_lines=exac_handle,
mim2gene_lines=mim2gene_handle,
genemap_lines=genemap_handle,
hpo_lines=hpo_genes_handle,
)
load_hgnc_genes(adapter, genes37, build='37')
hpo_terms_handle = context.obj['hpo_terms']
disease_handle = context.obj['disease_terms']
hpo_disease_handle = context.obj['hpodiseases']
load_hpo(
adapter=adapter,
hpo_lines=hpo_terms_handle,
disease_lines=disease_handle,
hpo_disease_lines=hpo_disease_handle
)
panel_info = {
'date': datetime.datetime.now(),
'file': panel_path,
'type': 'clinical',
'institute': 'cust000',
'version': '1.0',
'panel_name': 'panel1',
'full_name': 'Test panel'
}
parsed_panel = parse_gene_panel(panel_info)
panel_obj = build_panel(parsed_panel, adapter)
load_panel(
adapter=adapter,
panel_info=panel_info
)
case_handle = get_file_handle(load_path)
case_data = yaml.load(case_handle)
case_data['vcf_snv'] = clinical_snv_path
case_data['vcf_sv'] = clinical_sv_path
case_data['vcf_snv_research'] = research_snv_path
case_data['vcf_sv_research'] = research_sv_path
case_data['madeline'] = madeline_path
load_scout(adapter, case_data)
log.info("Creating indexes")
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('chromosome', pymongo.ASCENDING)])
log.info("hgnc gene index created")
log.info("Scout demo instance setup successful")
def load_omim_panel(self, api_key, institute=None):
"""Create and load the OMIM-AUTO panel"""
existing_panel = self.gene_panel(panel_id='OMIM-AUTO')
if not existing_panel:
LOG.warning("OMIM-AUTO does not exists in database")
LOG.info('Creating a first version')
version = 1.0
if existing_panel:
version = float(math.floor(existing_panel['version']) + 1)
LOG.info("Setting version to %s", version)
try:
mim_files = fetch_mim_files(api_key=api_key, genemap2=True, mim2genes=True)
except Exception as err:
raise err
date_string = None
# Get the correct date when omim files where released
for line in mim_files['genemap2']:
if 'Generated' in line:
date_string = line.split(':')[-1].lstrip().rstrip()
date_obj = get_date(date_string)
if existing_panel:
if existing_panel['date'] == date_obj:
LOG.warning("There is no new version of OMIM")
return
panel_data = {}
panel_data['path'] = None
panel_data['type'] = 'clinical'
panel_data['date'] = date_obj
panel_data['panel_id'] = 'OMIM-AUTO'
panel_data['institute'] = institute or 'cust002'
panel_data['version'] = version
panel_data['display_name'] = 'OMIM-AUTO'
panel_data['genes'] = []
alias_genes = self.genes_by_alias()
genes = get_omim_panel_genes(
genemap2_lines = mim_files['genemap2'],
mim2gene_lines = mim_files['mim2genes'],
alias_genes = alias_genes,
)
for gene in genes:
panel_data['genes'].append(gene)
panel_obj = build_panel(panel_data, self)
if existing_panel:
new_genes = self.compare_mim_panels(existing_panel, panel_obj)
if new_genes:
self.update_mim_version(new_genes, panel_obj, old_version=existing_panel['version'])
else:
LOG.info("The new version of omim does not differ from the old one")
LOG.info("No update is added")
return
self.add_gene_panel(panel_obj)
