def real_gene_database(
request,
real_institute_database,
genes37_handle,
hgnc_handle,
exac_handle,
mim2gene_handle,
genemap_handle,
hpo_genes_handle,
):
"Returns an adapter to a database populated with user, institute, case and genes"
adapter = real_institute_database
load_hgnc_genes(
adapter=adapter,
ensembl_lines=genes37_handle,
hgnc_lines=hgnc_handle,
exac_lines=exac_handle,
mim2gene_lines=mim2gene_handle,
genemap_lines=genemap_handle,
hpo_lines=hpo_genes_handle,
build="37",
)
LOG.info("Creating index on hgnc collection")
adapter.hgnc_collection.create_index([("build", pymongo.ASCENDING),
("hgnc_symbol", pymongo.ASCENDING)])
LOG.info("Index done")
return adapter
def real_gene_database(request, real_institute_database, genes):
"Returns an adapter to a database populated with user, institute and case"
adapter = real_institute_database
load_hgnc_genes(adapter, genes)
logger.info("Creating index on hgnc collection")
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('hgnc_symbol', pymongo.ASCENDING)])
logger.info("Index done")
return adapter
def genes(context, build, api_key):
"""
Load the hgnc aliases to the mongo database.
"""
adapter = context.obj['adapter']
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key to load the omim gene panel")
context.abort()
try:
mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
except Exception as err:
LOG.warning(err)
context.abort()
LOG.warning("Dropping all gene information")
adapter.drop_genes(build)
LOG.info("Genes dropped")
hpo_genes = fetch_hpo_genes()
if build:
builds = [build]
else:
builds = ['37', '38']
for build in builds:
LOG.info("Loading hgnc file from {0}".format(hgnc_path))
hgnc_handle = get_file_handle(hgnc_path)
ensembl_handle = None
if build == '37':
ensembl_handle = get_file_handle(transcripts37_path)
elif build == '38':
ensembl_handle = get_file_handle(transcripts38_path)
LOG.info("Loading exac gene file from {0}".format(exac_path))
exac_handle = get_file_handle(exac_path)
genes = link_genes(
ensembl_lines=ensembl_handle,
hgnc_lines=hgnc_handle,
exac_lines=exac_handle,
mim2gene_lines=mim_files['mim2genes'],
genemap_lines=mim_files['genemap2'],
hpo_lines=hpo_genes
)
load_hgnc_genes(adapter=adapter, genes=genes, build=build)
def genes(ctx, update, build):
"""
Load the hgnc aliases to the mongo database.
"""
adapter = ctx.obj['adapter']
# Test if the genes are loaded
nr_present_genes = adapter.nr_genes(build=build)
if nr_present_genes > 0:
if update:
logger.warning("Dropping all gene information")
adapter.drop_genes()
logger.info("Genes dropped")
else:
logger.info("Genes are already loaded")
logger.info("If you wish to update genes use '--update'")
ctx.abort()
logger.info("Loading hgnc file from {0}".format(hgnc_path))
hgnc_handle = get_file_handle(hgnc_path)
if build == '37':
logger.info("Loading ensembl transcript file from {0}".format(
transcripts37_path))
ensembl_handle = get_file_handle(transcripts37_path)
else:
ensembl_handle = get_file_handle(transcripts38_path)
logger.info("Loading exac gene file from {0}".format(
exac_path))
exac_handle = get_file_handle(exac_path)
logger.info("Loading mim information from files {0}, {1}".format(
mim2gene_path, genemap2_path))
mim2gene_handle = get_file_handle(mim2gene_path)
genemap_handle = get_file_handle(genemap2_path)
hpo_handle = get_file_handle(hpogenes_path)
genes = link_genes(
ensembl_lines=ensembl_handle,
hgnc_lines=hgnc_handle,
exac_lines=exac_handle,
mim2gene_lines=mim2gene_handle,
genemap_lines=genemap_handle,
hpo_lines=hpo_handle
)
load_hgnc_genes(adapter=adapter, genes=genes, build=build)
def real_gene_database(
real_institute_database,
genes37_handle,
hgnc_handle,
exac_handle,
mim2gene_handle,
genemap_handle,
hpo_genes_handle,
):
"Returns an adapter to a database populated with user, institute, case and genes"
adapter = real_institute_database
load_hgnc_genes(
adapter=adapter,
ensembl_lines=genes37_handle,
hgnc_lines=hgnc_handle,
exac_lines=exac_handle,
mim2gene_lines=mim2gene_handle,
genemap_lines=genemap_handle,
hpo_lines=hpo_genes_handle,
build="37",
)
return adapter
def gene_database(request, institute_database, genes):
"Returns an adapter to a database populated with user, institute, case and genes"
adapter = institute_database
gene_objs = load_hgnc_genes(adapter=adapter, genes=genes, build='37')
LOG.info("Creating index on hgnc collection")
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('hgnc_symbol', pymongo.ASCENDING)])
transcripts_handle = get_file_handle(transcripts37_reduced_path)
load_transcripts(adapter, transcripts_handle, build='37')
adapter.transcript_collection.create_index([('build', pymongo.ASCENDING),
('hgnc_id', pymongo.ASCENDING)
])
LOG.info("Index done")
return adapter
def setup_scout(
adapter,
institute_id="cust000",
user_name="Clark Kent",
user_mail="*****@*****.**",
api_key=None,
demo=False,
resource_files=None,
):
"""Function to setup a working scout instance.
WARNING: If the instance is populated all collections will be deleted
Build insert a institute and an admin user.
There are multiple sources of information that is used by scout and that needs to exist for
scout to work proper.
Genes:
Scout uses HGNC as the source for gene identifiers en ensembl as source for coordinates.
Additional information of disease connections for genes if fetched from OMIM.
Link between hpo terms and genes is fetched from HPO
For more details check the documentation.
"""
LOG.info("Check if there was a database, delete if existing")
existing_database = False
for collection_name in adapter.db.list_collection_names():
if collection_name.startswith("system"):
continue
LOG.info("Deleting collection %s", collection_name)
adapter.db.drop_collection(collection_name)
existing_database = True
if existing_database:
LOG.info("Database deleted")
institute_obj = build_institute(
internal_id=institute_id,
display_name=institute_id,
sanger_recipients=[user_mail],
)
adapter.add_institute(institute_obj)
user_obj = dict(
_id=user_mail,
email=user_mail,
name=user_name,
roles=["admin"],
institutes=[institute_id],
)
adapter.add_user(user_obj)
resource_files = resource_files or {}
if demo:
resource_files = demo_files
mim2gene_lines = None
genemap_lines = None
mim2gene_path = resource_files.get("mim2gene_path")
genemap_path = resource_files.get("genemap_path")
if genemap_path and mim2gene_path:
mim2gene_lines = [line for line in get_file_handle(mim2gene_path)]
genemap_lines = [line for line in get_file_handle(genemap_path)]
if (genemap_lines is None) and api_key:
try:
mim_files = fetch_mim_files(api_key, mim2genes=True, genemap2=True)
except Exception as err:
LOG.warning(err)
raise err
mim2gene_lines = mim_files["mim2genes"]
genemap_lines = mim_files["genemap2"]
if resource_files.get("hpogenes_path"):
hpo_gene_lines = [
line
for line in get_file_handle(resource_files.get("hpogenes_path"))
]
else:
hpo_gene_lines = fetch_genes_to_hpo_to_disease()
if resource_files.get("hgnc_path"):
hgnc_lines = [
line for line in get_file_handle(resource_files.get("hgnc_path"))
]
else:
hgnc_lines = fetch_hgnc()
if resource_files.get("exac_path"):
exac_lines = [
line for line in get_file_handle(resource_files.get("exac_path"))
]
else:
exac_lines = fetch_exac_constraint()
# Load cytobands into cytoband collection
for genome_build, cytobands_path in cytoband_files.items():
load_cytobands(cytobands_path, genome_build, adapter)
builds = ["37", "38"]
for build in builds:
genes_path = "genes{}_path".format(build)
if resource_files.get(genes_path):
ensembl_genes = get_file_handle(resource_files[genes_path])
else:
ensembl_genes = fetch_ensembl_genes(build=build)
hgnc_genes = load_hgnc_genes(
adapter=adapter,
ensembl_lines=ensembl_genes,
hgnc_lines=hgnc_lines,
exac_lines=exac_lines,
mim2gene_lines=mim2gene_lines,
genemap_lines=genemap_lines,
hpo_lines=hpo_gene_lines,
build=build,
)
# Create a map from ensembl ids to gene objects
ensembl_genes = {}
for gene_obj in hgnc_genes:
ensembl_id = gene_obj["ensembl_id"]
ensembl_genes[ensembl_id] = gene_obj
tx_path = "transcripts{}_path".format(build)
if resource_files.get(tx_path):
ensembl_transcripts = get_file_handle(resource_files[tx_path])
else:
ensembl_transcripts = fetch_ensembl_transcripts(build=build)
# Load the transcripts for a certain build
transcripts = load_transcripts(adapter, ensembl_transcripts, build,
ensembl_genes)
hpo_terms_handle = None
if resource_files.get("hpoterms_path"):
hpo_terms_handle = get_file_handle(resource_files["hpoterms_path"])
hpo_to_genes_handle = None
if resource_files.get("hpo_to_genes_path"):
hpo_to_genes_handle = get_file_handle(
resource_files["hpo_to_genes_path"])
hpo_disease_handle = None
if resource_files.get("hpo_disease_path"):
hpo_disease_handle = get_file_handle(
resource_files["hpo_disease_path"])
load_hpo(
adapter=adapter,
disease_lines=genemap_lines,
hpo_lines=hpo_terms_handle,
hpo_gene_lines=hpo_to_genes_handle,
)
# If demo we load a gene panel and some case information
if demo:
parsed_panel = parse_gene_panel(
path=panel_path,
institute="cust000",
panel_id="panel1",
version=1.0,
display_name="Test panel",
)
adapter.load_panel(parsed_panel)
case_handle = get_file_handle(load_path)
case_data = yaml.load(case_handle, Loader=yaml.FullLoader)
config_data = parse_case_data(config=case_data)
adapter.load_case(config_data)
LOG.info("Creating indexes")
adapter.load_indexes()
LOG.info("Scout instance setup successful")
def genes(build, api_key):
"""
Load the hgnc aliases to the mongo database.
"""
LOG.info("Running scout update genes")
adapter = store
# Fetch the omim information
api_key = api_key or current_app.config.get('OMIM_API_KEY')
if not api_key:
LOG.warning(
"Please provide a omim api key to load the omim gene panel")
raise click.Abort()
try:
mim_files = fetch_mim_files(api_key,
mim2genes=True,
morbidmap=True,
genemap2=True)
except Exception as err:
LOG.warning(err)
raise click.Abort()
LOG.warning("Dropping all gene information")
adapter.drop_genes(build)
LOG.info("Genes dropped")
LOG.warning("Dropping all transcript information")
adapter.drop_transcripts(build)
LOG.info("transcripts dropped")
hpo_genes = fetch_hpo_genes()
if build:
builds = [build]
else:
builds = ['37', '38']
hgnc_lines = fetch_hgnc()
exac_lines = fetch_exac_constraint()
for build in builds:
ensembl_genes = fetch_ensembl_genes(build=build)
# load the genes
hgnc_genes = load_hgnc_genes(
adapter=adapter,
ensembl_lines=ensembl_genes,
hgnc_lines=hgnc_lines,
exac_lines=exac_lines,
mim2gene_lines=mim_files['mim2genes'],
genemap_lines=mim_files['genemap2'],
hpo_lines=hpo_genes,
build=build,
)
ensembl_genes = {}
for gene_obj in hgnc_genes:
ensembl_id = gene_obj['ensembl_id']
ensembl_genes[ensembl_id] = gene_obj
# Fetch the transcripts from ensembl
ensembl_transcripts = fetch_ensembl_transcripts(build=build)
transcripts = load_transcripts(adapter, ensembl_transcripts, build,
ensembl_genes)
adapter.update_indexes()
LOG.info("Genes, transcripts and Exons loaded")
def genes(context, build, api_key):
"""
Load the hgnc aliases to the mongo database.
"""
LOG.info("Running scout update genes")
adapter = context.obj['adapter']
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key to load the omim gene panel")
context.abort()
try:
mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
except Exception as err:
LOG.warning(err)
context.abort()
LOG.warning("Dropping all gene information")
adapter.drop_genes(build)
LOG.info("Genes dropped")
LOG.warning("Dropping all transcript information")
adapter.drop_transcripts(build)
LOG.info("transcripts dropped")
hpo_genes = fetch_hpo_genes()
if build:
builds = [build]
else:
builds = ['37', '38']
hgnc_lines = fetch_hgnc()
exac_lines = fetch_exac_constraint()
for build in builds:
ensembl_genes = fetch_ensembl_genes(build=build)
# load the genes
hgnc_genes = load_hgnc_genes(
adapter=adapter,
ensembl_lines=ensembl_genes,
hgnc_lines=hgnc_lines,
exac_lines=exac_lines,
mim2gene_lines=mim_files['mim2genes'],
genemap_lines=mim_files['genemap2'],
hpo_lines=hpo_genes,
build=build,
)
ensembl_genes = {}
for gene_obj in hgnc_genes:
ensembl_id = gene_obj['ensembl_id']
ensembl_genes[ensembl_id] = gene_obj
# Fetch the transcripts from ensembl
ensembl_transcripts = fetch_ensembl_transcripts(build=build)
transcripts = load_transcripts(adapter, ensembl_transcripts, build, ensembl_genes)
adapter.update_indexes()
LOG.info("Genes, transcripts and Exons loaded")
def genes(build, api_key):
"""
Load the hgnc aliases to the mongo database.
"""
LOG.info("Running scout update genes")
adapter = store
# Fetch the omim information
api_key = api_key or current_app.config.get("OMIM_API_KEY")
mim_files = {}
if not api_key:
LOG.warning("No omim api key provided, Please not that some information will be missing")
else:
try:
mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
except Exception as err:
LOG.warning(err)
raise click.Abort()
LOG.warning("Dropping all gene information")
adapter.drop_genes(build)
LOG.info("Genes dropped")
LOG.warning("Dropping all transcript information")
adapter.drop_transcripts(build)
LOG.info("transcripts dropped")
hpo_genes = fetch_genes_to_hpo_to_disease()
if build:
builds = [build]
else:
builds = ["37", "38"]
hgnc_lines = fetch_hgnc()
exac_lines = fetch_exac_constraint()
for build in builds:
ensembl_genes = fetch_ensembl_genes(build=build)
# load the genes
hgnc_genes = load_hgnc_genes(
adapter=adapter,
ensembl_lines=ensembl_genes,
hgnc_lines=hgnc_lines,
exac_lines=exac_lines,
mim2gene_lines=mim_files.get("mim2genes"),
genemap_lines=mim_files.get("genemap2"),
hpo_lines=hpo_genes,
build=build,
)
ensembl_genes = {}
for gene_obj in hgnc_genes:
ensembl_id = gene_obj["ensembl_id"]
ensembl_genes[ensembl_id] = gene_obj
# Fetch the transcripts from ensembl
ensembl_transcripts = fetch_ensembl_transcripts(build=build)
transcripts = load_transcripts(adapter, ensembl_transcripts, build, ensembl_genes)
adapter.update_indexes()
LOG.info("Genes, transcripts and Exons loaded")
def database(context, institute_name, user_name, user_mail):
"""Setup a scout database"""
log.info("Running scout setup database")
institute_name = institute_name or context.obj['institute_name']
user_name = user_name or context.obj['user_name']
user_mail = user_mail or 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')
genes38 = link_genes(
ensembl_lines=transcripts38_handle,
hgnc_lines=context.obj['hgnc38'],
exac_lines=context.obj['exac38'],
mim2gene_lines=context.obj['mim2gene38'],
genemap_lines=context.obj['genemap2_38'],
hpo_lines=context.obj['hpogenes_38'],
)
load_hgnc_genes(adapter, genes38, build='38')
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
)
log.info("Creating indexes")
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('chromosome', pymongo.ASCENDING)])
log.info("hgnc gene index created")
log.info("Scout instance setup successful")
def setup_scout(adapter,
institute_id='cust000',
user_name='Clark Kent',
user_mail='*****@*****.**',
api_key=None,
demo=False):
"""docstring for setup_scout"""
########################## Delete previous information ##########################
LOG.info("Deleting previous database")
for collection_name in adapter.db.collection_names():
if not collection_name.startswith('system'):
LOG.info("Deleting collection %s", collection_name)
adapter.db.drop_collection(collection_name)
LOG.info("Database deleted")
########################## Add a institute ##########################
#####################################################################
# Build a institute with id institute_name
institute_obj = build_institute(internal_id=institute_id,
display_name=institute_id,
sanger_recipients=[user_mail])
# Add the institute to database
adapter.add_institute(institute_obj)
########################## Add a User ###############################
#####################################################################
# Build a user obj
user_obj = dict(_id=user_mail,
email=user_mail,
name=user_name,
roles=['admin'],
institutes=[institute_id])
adapter.add_user(user_obj)
### Get the mim information ###
if not demo:
# Fetch the mim files
try:
mim_files = fetch_mim_files(api_key,
mim2genes=True,
morbidmap=True,
genemap2=True)
except Exception as err:
LOG.warning(err)
context.abort()
mim2gene_lines = mim_files['mim2genes']
genemap_lines = mim_files['genemap2']
# Fetch the genes to hpo information
hpo_gene_lines = fetch_hpo_genes()
# Fetch the latest version of the hgnc information
hgnc_lines = fetch_hgnc()
# Fetch the latest exac pli score information
exac_lines = fetch_exac_constraint()
else:
mim2gene_lines = [
line for line in get_file_handle(mim2gene_reduced_path)
]
genemap_lines = [
line for line in get_file_handle(genemap2_reduced_path)
]
# Fetch the genes to hpo information
hpo_gene_lines = [
line for line in get_file_handle(hpogenes_reduced_path)
]
# Fetch the reduced hgnc information
hgnc_lines = [line for line in get_file_handle(hgnc_reduced_path)]
# Fetch the latest exac pli score information
exac_lines = [line for line in get_file_handle(exac_reduced_path)]
builds = ['37', '38']
################## Load Genes and transcripts #######################
#####################################################################
for build in builds:
# Fetch the ensembl information
if not demo:
ensembl_genes = fetch_ensembl_genes(build=build)
else:
ensembl_genes = get_file_handle(genes37_reduced_path)
# load the genes
hgnc_genes = load_hgnc_genes(
adapter=adapter,
ensembl_lines=ensembl_genes,
hgnc_lines=hgnc_lines,
exac_lines=exac_lines,
mim2gene_lines=mim2gene_lines,
genemap_lines=genemap_lines,
hpo_lines=hpo_gene_lines,
build=build,
)
# Create a map from ensembl ids to gene objects
ensembl_genes = {}
for gene_obj in hgnc_genes:
ensembl_id = gene_obj['ensembl_id']
ensembl_genes[ensembl_id] = gene_obj
# Fetch the transcripts from ensembl
if not demo:
ensembl_transcripts = fetch_ensembl_transcripts(build=build)
else:
ensembl_transcripts = get_file_handle(transcripts37_reduced_path)
# Load the transcripts for a certain build
transcripts = load_transcripts(adapter, ensembl_transcripts, build,
ensembl_genes)
hpo_terms_handle = None
hpo_to_genes_handle = None
hpo_disease_handle = None
if demo:
hpo_terms_handle = get_file_handle(hpoterms_reduced_path)
hpo_to_genes_handle = get_file_handle(hpo_to_genes_reduced_path)
hpo_disease_handle = get_file_handle(
hpo_phenotype_to_terms_reduced_path)
load_hpo(adapter=adapter,
hpo_lines=hpo_terms_handle,
hpo_gene_lines=hpo_to_genes_handle,
disease_lines=genemap_lines,
hpo_disease_lines=hpo_disease_handle)
# If demo we load a gene panel and some case information
if demo:
parsed_panel = parse_gene_panel(path=panel_path,
institute='cust000',
panel_id='panel1',
version=1.0,
display_name='Test panel')
adapter.load_panel(parsed_panel)
case_handle = get_file_handle(load_path)
case_data = yaml.load(case_handle)
adapter.load_case(case_data)
LOG.info("Creating indexes")
adapter.load_indexes()
LOG.info("Scout instance setup successful")
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 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
LOG.info("Loading hgnc genes from %s", hgnc_reduced_path)
hgnc_handle = get_file_handle(hgnc_reduced_path)
hgnc38 = get_file_handle(hgnc_reduced_path)
LOG.info("Loading exac genes from %s", exac_reduced_path)
exac_handle = get_file_handle(exac_reduced_path)
exac38 = get_file_handle(exac_reduced_path)
LOG.info("Loading mim2gene info from %s", mim2gene_reduced_path)
mim2gene_handle = get_file_handle(mim2gene_reduced_path)
mim2gene38 = get_file_handle(mim2gene_reduced_path)
LOG.info("Loading genemap info from %s", genemap2_reduced_path)
genemap_handle = get_file_handle(genemap2_reduced_path)
genemap38 = get_file_handle(genemap2_reduced_path)
LOG.info("Loading hpo gene info from %s", hpogenes_reduced_path)
hpo_genes_handle = get_file_handle(hpogenes_reduced_path)
hpo_to_genes_handle = get_file_handle(hpo_to_genes_reduced_path)
hpogenes38 = get_file_handle(hpogenes_reduced_path)
LOG.info("Loading hpo disease info from %s", hpo_phenotype_to_terms_reduced_path)
hpo_disease_handle = get_file_handle(hpo_phenotype_to_terms_reduced_path)
LOG.info("Loading hpo terms from %s", hpoterms_reduced_path)
hpo_terms_handle = get_file_handle(hpoterms_reduced_path)
LOG.info("Loading omim disease info from %s", genemap2_reduced_path)
disease_handle = get_file_handle(genemap2_reduced_path)
LOG.info("Loading transcripts build 37 info from %s", transcripts37_reduced_path)
transcripts37_handle = get_file_handle(transcripts37_reduced_path)
transcripts38_handle = get_file_handle(transcripts38_reduced_path)
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')
load_hpo(
adapter=adapter,
hpo_lines=hpo_terms_handle,
hpo_gene_lines=hpo_to_genes_handle,
disease_lines=disease_handle,
hpo_disease_lines=hpo_disease_handle
)
adapter.load_panel(
path=panel_path,
institute='cust000',
panel_id='panel1',
date=datetime.datetime.now(),
panel_type='clinical',
version=1.0,
display_name='Test panel'
)
case_handle = get_file_handle(load_path)
case_data = yaml.load(case_handle)
adapter.load_case(case_data)
LOG.info("Creating indexes")
adapter.load_indexes()
LOG.info("Scout demo instance setup successful")
def setup_scout(adapter, institute_id='cust000', user_name='Clark Kent',
user_mail='*****@*****.**', api_key=None, demo=False):
"""docstring for setup_scout"""
########################## Delete previous information ##########################
LOG.info("Deleting previous database")
for collection_name in adapter.db.collection_names():
if not collection_name.startswith('system'):
LOG.info("Deleting collection %s", collection_name)
adapter.db.drop_collection(collection_name)
LOG.info("Database deleted")
########################## Add a institute ##########################
#####################################################################
# Build a institute with id institute_name
institute_obj = build_institute(
internal_id=institute_id,
display_name=institute_id,
sanger_recipients=[user_mail]
)
# Add the institute to database
adapter.add_institute(institute_obj)
########################## Add a User ###############################
#####################################################################
# Build a user obj
user_obj = dict(
_id=user_mail,
email=user_mail,
name=user_name,
roles=['admin'],
institutes=[institute_id]
)
adapter.add_user(user_obj)
### Get the mim information ###
if not demo:
# Fetch the mim files
try:
mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
except Exception as err:
LOG.warning(err)
raise err
mim2gene_lines = mim_files['mim2genes']
genemap_lines = mim_files['genemap2']
# Fetch the genes to hpo information
hpo_gene_lines = fetch_hpo_genes()
# Fetch the latest version of the hgnc information
hgnc_lines = fetch_hgnc()
# Fetch the latest exac pli score information
exac_lines = fetch_exac_constraint()
else:
mim2gene_lines = [line for line in get_file_handle(mim2gene_reduced_path)]
genemap_lines = [line for line in get_file_handle(genemap2_reduced_path)]
# Fetch the genes to hpo information
hpo_gene_lines = [line for line in get_file_handle(hpogenes_reduced_path)]
# Fetch the reduced hgnc information
hgnc_lines = [line for line in get_file_handle(hgnc_reduced_path)]
# Fetch the latest exac pli score information
exac_lines = [line for line in get_file_handle(exac_reduced_path)]
builds = ['37', '38']
################## Load Genes and transcripts #######################
#####################################################################
for build in builds:
# Fetch the ensembl information
if not demo:
ensembl_genes = fetch_ensembl_genes(build=build)
else:
ensembl_genes = get_file_handle(genes37_reduced_path)
# load the genes
hgnc_genes = load_hgnc_genes(
adapter=adapter,
ensembl_lines=ensembl_genes,
hgnc_lines=hgnc_lines,
exac_lines=exac_lines,
mim2gene_lines=mim2gene_lines,
genemap_lines=genemap_lines,
hpo_lines=hpo_gene_lines,
build=build,
)
# Create a map from ensembl ids to gene objects
ensembl_genes = {}
for gene_obj in hgnc_genes:
ensembl_id = gene_obj['ensembl_id']
ensembl_genes[ensembl_id] = gene_obj
# Fetch the transcripts from ensembl
if not demo:
ensembl_transcripts = fetch_ensembl_transcripts(build=build)
else:
ensembl_transcripts = get_file_handle(transcripts37_reduced_path)
# Load the transcripts for a certain build
transcripts = load_transcripts(adapter, ensembl_transcripts, build, ensembl_genes)
hpo_terms_handle = None
hpo_to_genes_handle = None
hpo_disease_handle = None
if demo:
hpo_terms_handle = get_file_handle(hpoterms_reduced_path)
hpo_to_genes_handle = get_file_handle(hpo_to_genes_reduced_path)
hpo_disease_handle = get_file_handle(hpo_phenotype_to_terms_reduced_path)
load_hpo(
adapter=adapter,
hpo_lines=hpo_terms_handle,
hpo_gene_lines=hpo_to_genes_handle,
disease_lines=genemap_lines,
hpo_disease_lines=hpo_disease_handle
)
# If demo we load a gene panel and some case information
if demo:
parsed_panel = parse_gene_panel(
path=panel_path,
institute='cust000',
panel_id='panel1',
version=1.0,
display_name='Test panel'
)
adapter.load_panel(parsed_panel)
case_handle = get_file_handle(load_path)
case_data = yaml.load(case_handle, Loader=yaml.FullLoader)
adapter.load_case(case_data)
LOG.info("Creating indexes")
adapter.load_indexes()
LOG.info("Scout instance setup successful")
def genes(build, downloads_folder, api_key):
"""
Load the hgnc aliases to the mongo database.
"""
LOG.info("Running scout update genes")
adapter = store
builds = [build] if build else ["37", "38"]
api_key = api_key or current_app.config.get("OMIM_API_KEY")
resources = {}
# If required resources are missing, download them to a temporary directory
if downloads_folder is None:
with tempfile.TemporaryDirectory() as tempdir:
try:
download_resources(tempdir, api_key, builds)
except Exception as ex:
LOG.error(ex)
fetch_downloaded_resources(resources, tempdir, builds)
else: # If resources have been previosly downloaded, read those file and return their lines
fetch_downloaded_resources(resources, downloads_folder, builds)
# Load genes and transcripts info
for genome_build in builds:
LOG.warning("Dropping all gene information")
adapter.drop_genes(genome_build)
LOG.warning("Dropping all transcript information")
adapter.drop_transcripts(genome_build)
ensembl_gene_res = (
resources.get("ensembl_genes_37")
if genome_build == "37" else resources.get("ensembl_genes_38")
) # It will be none if everything needs to be downloaded
# Load the genes
hgnc_genes = load_hgnc_genes(
adapter=adapter,
ensembl_lines=ensembl_gene_res,
hgnc_lines=resources.get("hgnc_lines"),
exac_lines=resources.get("exac_lines"),
mim2gene_lines=resources.get("mim2genes"),
genemap_lines=resources.get("genemap2"),
hpo_lines=resources.get("hpo_genes"),
build=genome_build,
)
ensembl_genes_dict = {}
for gene_obj in hgnc_genes:
ensembl_id = gene_obj["ensembl_id"]
ensembl_genes_dict[ensembl_id] = gene_obj
# Load the transcripts
ensembl_tx_res = (
resources.get("ensembl_transcripts_37") if genome_build == "37"
else resources.get("ensembl_transcripts_38")
) # It will be none if everything needs to be downloaded
load_transcripts(adapter, ensembl_tx_res, genome_build,
ensembl_genes_dict)
LOG.info("Genes and transcripts loaded")
def database(context, institute_name, user_name, user_mail, api_key):
"""Setup a scout database"""
LOG.info("Running scout setup database")
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key to load the omim gene panel")
context.abort()
try:
mim_files = fetch_mim_files(api_key, mim2genes=True, morbidmap=True, genemap2=True)
except Exception as err:
LOG.warning(err)
context.abort()
# for fn in mim_files:
# click.echo("{0}: {1}".format(fn, type(mim_files[fn])))
#
# context.abort()
institute_name = institute_name or context.obj['institute_name']
user_name = user_name or context.obj['user_name']
user_mail = user_mail or context.obj['user_mail']
adapter = context.obj['adapter']
LOG.info("Deleting previous database")
for collection_name in adapter.db.collection_names():
if not collection_name.startswith('system'):
LOG.info("Deleting collection %s", collection_name)
adapter.db.drop_collection(collection_name)
LOG.info("Database deleted")
LOG.info("Setting up database %s", context.obj['mongodb'])
# 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)
# Fetch the genes to hpo information
hpo_genes = fetch_hpo_genes()
# Load the genes and transcripts
genes37 = link_genes(
ensembl_lines=get_file_handle(transcripts37_path),
hgnc_lines=get_file_handle(hgnc_path),
exac_lines=get_file_handle(exac_path),
mim2gene_lines=mim_files['mim2genes'],
genemap_lines=mim_files['genemap2'],
hpo_lines=hpo_genes,
)
load_hgnc_genes(adapter, genes37, build='37')
genes38 = link_genes(
ensembl_lines=get_file_handle(transcripts38_path),
hgnc_lines=get_file_handle(hgnc_path),
exac_lines=get_file_handle(exac_path),
mim2gene_lines=mim_files['mim2genes'],
genemap_lines=mim_files['genemap2'],
hpo_lines=hpo_genes,
)
load_hgnc_genes(adapter, genes38, build='38')
load_hpo(
adapter=adapter,
disease_lines=mim_files['genemap2'],
)
LOG.info("Creating indexes")
adapter.load_indexes()
LOG.info("Scout instance setup successful")
