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 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)
