def gene_variants(institute_id):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj = institute_and_case(store, institute_id)
# populate form, conditional on request method
if (request.method == "POST"):
form = GeneVariantFiltersForm(request.form)
else:
form = GeneVariantFiltersForm(request.args)
variant_type = form.data.get('variant_type', 'clinical')
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
data = {}
if (form.hgnc_symbols.data) and len(form.hgnc_symbols.data) > 0:
is_clinical = form.data.get('variant_type', 'clinical') == 'clinical'
clinical_symbols = store.clinical_symbols(
case_obj) if is_clinical else None
for hgnc_symbol in form.hgnc_symbols.data:
if hgnc_symbol.isdigit():
hgnc_gene = store.hgnc_gene(int(hgnc_symbol))
if hgnc_gene is None:
not_found_ids.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
not_found_symbols.append(hgnc_symbol)
elif is_clinical and (hgnc_symbol not in clinical_symbols):
non_clinical_symbols.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_symbol)
if (not_found_ids):
flash("HGNC id not found: {}".format(", ".join(not_found_ids)),
'warning')
if (not_found_symbols):
flash(
"HGNC symbol not found: {}".format(
", ".join(not_found_symbols)), 'warning')
if (non_clinical_symbols):
flash(
"Gene not included in clinical list: {}".format(
", ".join(non_clinical_symbols)), 'warning')
form.hgnc_symbols.data = hgnc_symbols
log.debug("query {}".format(form.data))
variants_query = store.gene_variants(query=form.data,
category='snv',
variant_type=variant_type)
data = controllers.gene_variants(store, variants_query, page)
return dict(institute=institute_obj, form=form, page=page, **data)
def gene_variants(institute_id):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj = institute_and_case(store, institute_id)
# populate form, conditional on request method
if(request.method == "POST"):
form = GeneVariantFiltersForm(request.form)
else:
form = GeneVariantFiltersForm(request.args)
variant_type = form.data.get('variant_type', 'clinical')
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
data = {}
if (form.hgnc_symbols.data) and len(form.hgnc_symbols.data) > 0:
is_clinical = form.data.get('variant_type', 'clinical') == 'clinical'
clinical_symbols = store.clinical_symbols(case_obj) if is_clinical else None
for hgnc_symbol in form.hgnc_symbols.data:
if hgnc_symbol.isdigit():
hgnc_gene = store.hgnc_gene(int(hgnc_symbol))
if hgnc_gene is None:
not_found_ids.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
not_found_symbols.append(hgnc_symbol)
elif is_clinical and (hgnc_symbol not in clinical_symbols):
non_clinical_symbols.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_symbol)
if (not_found_ids):
flash("HGNC id not found: {}".format(", ".join(not_found_ids)), 'warning')
if (not_found_symbols):
flash("HGNC symbol not found: {}".format(", ".join(not_found_symbols)), 'warning')
if (non_clinical_symbols):
flash("Gene not included in clinical list: {}".format(", ".join(non_clinical_symbols)), 'warning')
form.hgnc_symbols.data = hgnc_symbols
log.debug("query {}".format(form.data))
variants_query = store.gene_variants(query=form.data, category='snv',
variant_type=variant_type)
data = controllers.gene_variants(store, variants_query, page)
return dict(institute=institute_obj, form=form, page=page, **data)
def gene_variants(institute_id):
"""Display a list of SNV variants."""
page = int(request.form.get("page", 1))
institute_obj = institute_and_case(store, institute_id)
# populate form, conditional on request method
if request.method == "POST":
form = GeneVariantFiltersForm(request.form)
else:
form = GeneVariantFiltersForm(request.args)
if form.variant_type.data == []:
form.variant_type.data = ["clinical"]
variant_type = form.data.get("variant_type")
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
data = {}
if (form.hgnc_symbols.data) and len(form.hgnc_symbols.data) > 0:
is_clinical = form.data.get("variant_type", "clinical") == "clinical"
# clinical_symbols = store.clinical_symbols(case_obj) if is_clinical else None
for hgnc_symbol in form.hgnc_symbols.data:
if hgnc_symbol.isdigit():
hgnc_gene = store.hgnc_gene(int(hgnc_symbol))
if hgnc_gene is None:
not_found_ids.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_gene["hgnc_symbol"])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
not_found_symbols.append(hgnc_symbol)
# elif is_clinical and (hgnc_symbol not in clinical_symbols):
# non_clinical_symbols.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_symbol)
if not_found_ids:
flash("HGNC id not found: {}".format(", ".join(not_found_ids)),
"warning")
if not_found_symbols:
flash(
"HGNC symbol not found: {}".format(
", ".join(not_found_symbols)),
"warning",
)
if non_clinical_symbols:
flash(
"Gene not included in clinical list: {}".format(
", ".join(non_clinical_symbols)),
"warning",
)
form.hgnc_symbols.data = hgnc_symbols
LOG.debug("query {}".format(form.data))
variants_query = store.gene_variants(
query=form.data,
institute_id=institute_id,
category="snv",
variant_type=variant_type,
)
data = controllers.gene_variants(store, variants_query, institute_id,
page)
return dict(institute=institute_obj, form=form, page=page, **data)
def gene_variants(institute_id):
"""Display a list of SNV variants."""
page = int(request.form.get("page", 1))
institute_obj = institute_and_case(store, institute_id)
# populate form, conditional on request method
if request.method == "POST":
form = GeneVariantFiltersForm(request.form)
else:
form = GeneVariantFiltersForm(request.args)
if form.variant_type.data == []:
form.variant_type.data = ["clinical"]
variant_type = form.data.get("variant_type")
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
data = {}
if (form.hgnc_symbols.data) and len(form.hgnc_symbols.data) > 0:
is_clinical = form.data.get("variant_type", "clinical") == "clinical"
# clinical_symbols = store.clinical_symbols(case_obj) if is_clinical else None
for hgnc_symbol in form.hgnc_symbols.data:
if hgnc_symbol.isdigit():
hgnc_gene = store.hgnc_gene(int(hgnc_symbol))
if hgnc_gene is None:
not_found_ids.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_gene["hgnc_symbol"])
elif store.hgnc_genes_find_one(hgnc_symbol) is None:
not_found_symbols.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_symbol)
if not_found_ids:
flash("HGNC id not found: {}".format(", ".join(not_found_ids)),
"warning")
if not_found_symbols:
flash(
"HGNC symbol not found: {}".format(
", ".join(not_found_symbols)), "warning")
if non_clinical_symbols:
flash(
"Gene not included in clinical list: {}".format(
", ".join(non_clinical_symbols)),
"warning",
)
if hgnc_symbols == []:
# If there are not genes to search, return to previous page with a warning
flash("No valid gene provided for variant search.", "warning")
return redirect(request.referrer)
form.hgnc_symbols.data = hgnc_symbols
variants_query = store.gene_variants(query=form.data,
institute_id=institute_id,
category="snv",
variant_type=variant_type)
result_size = store.count_gene_variants(query=form.data,
institute_id=institute_id,
category="snv",
variant_type=variant_type)
data = controllers.gene_variants(store, variants_query, result_size,
institute_id, page)
return dict(institute=institute_obj, form=form, page=page, **data)