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 variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_type = request.args.get('variant_type', 'clinical')
# Update filter settings if Clinical Filter was requested
default_panels = []
for panel in case_obj['panels']:
if panel.get('is_default'):
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type':
'clinical',
'region_annotations': ['exonic', 'splicing'],
'functional_annotations':
SEVERE_SO_TERMS,
'clinsig': [4, 5],
'clinsig_confident_always_returned':
True,
'gnomad_frequency':
str(institute_obj['frequency_cutoff']),
'variant_type':
'clinical',
'gene_panels':
default_panels
})
if (request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = FiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = FiltersForm(request.form)
else:
form = FiltersForm(request.args)
# populate available panel choices
available_panels = case_obj.get('panels', []) + [{
'panel_name': 'hpo',
'display_name': 'HPO'
}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
# upload gene panel if symbol file exists
if (request.files):
file = request.files[form.symbol_file.name]
if request.files and file and file.filename != '':
log.debug("Upload file request files: {0}".format(
request.files.to_dict()))
try:
stream = io.StringIO(file.stream.read().decode('utf-8'),
newline=None)
except UnicodeDecodeError as error:
flash("Only text files are supported!", 'warning')
return redirect(request.referrer)
hgnc_symbols_set = set(form.hgnc_symbols.data)
log.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set))
new_hgnc_symbols = controllers.upload_panel(store, institute_id,
case_name, stream)
hgnc_symbols_set.update(new_hgnc_symbols)
form.hgnc_symbols.data = hgnc_symbols_set
# reset gene panels
form.gene_panels.data = ''
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
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
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = {}
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
if form.data['chrom'] == 'MT':
# Return all MT variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query)
else:
# Return max 500 variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition',
'attachment',
filename=str(case_obj['display_name']) +
'-filtered_variants.csv')
# return a csv with the exported variants
return Response(generate(",".join(document_header), export_lines),
mimetype='text/csv',
headers=headers)
data = controllers.variants(store, institute_obj, case_obj, variants_query,
page)
return dict(institute=institute_obj,
case=case_obj,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.form.get("page", 1))
category = "snv"
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_type = request.args.get("variant_type", "clinical")
if request.form.get("hpo_clinical_filter"):
case_obj["hpo_clinical_filter"] = True
user_obj = store.user(current_user.email)
if request.method == "POST":
# If special filter buttons were selected:
form = controllers.populate_filters_form(
store, institute_obj, case_obj, user_obj, category, request.form
)
else:
form = FiltersForm(request.args)
# set form variant data type the first time around
form.variant_type.data = variant_type
# populate filters dropdown
available_filters = store.filters(institute_id, category)
form.filters.choices = [
(filter.get("_id"), filter.get("display_name")) for filter in available_filters
]
# populate available panel choices
available_panels = case_obj.get("panels", []) + [
{"panel_name": "hpo", "display_name": "HPO"}
]
panel_choices = [
(panel["panel_name"], panel["display_name"]) for panel in available_panels
]
form.gene_panels.choices = panel_choices
# update status of case if visited for the first time
controllers.activate_case(store, institute_obj, case_obj, current_user)
# upload gene panel if symbol file exists
if request.files:
file = request.files[form.symbol_file.name]
if request.files and file and file.filename != "":
log.debug("Upload file request files: {0}".format(request.files.to_dict()))
try:
stream = io.StringIO(file.stream.read().decode("utf-8"), newline=None)
except UnicodeDecodeError as error:
flash("Only text files are supported!", "warning")
return redirect(request.referrer)
hgnc_symbols_set = set(form.hgnc_symbols.data)
log.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set))
new_hgnc_symbols = controllers.upload_panel(
store, institute_id, case_name, stream
)
hgnc_symbols_set.update(new_hgnc_symbols)
form.hgnc_symbols.data = hgnc_symbols_set
# reset gene panels
form.gene_panels.data = ""
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
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 sum(1 for i in store.hgnc_genes(hgnc_symbol)) == 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
# handle HPO gene list separately
if "hpo" in form.data["gene_panels"]:
hpo_symbols = list(
set(term_obj["hgnc_symbol"] for term_obj in case_obj["dynamic_gene_list"])
)
current_symbols = set(hgnc_symbols)
current_symbols.update(hpo_symbols)
form.hgnc_symbols.data = list(current_symbols)
variants_query = store.variants(case_obj["_id"], query=form.data, category=category)
if request.form.get("export"):
return controllers.download_variants(store, case_obj, variants_query)
data = controllers.variants(store, institute_obj, case_obj, variants_query, page)
return dict(
institute=institute_obj,
case=case_obj,
form=form,
manual_rank_options=MANUAL_RANK_OPTIONS,
cancer_tier_options=CANCER_TIER_OPTIONS,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data
)
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.args.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
form = FiltersForm(request.args)
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in case_obj.get('panels', [])]
form.gene_panels.choices = panel_choices
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
if 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:
flash("HGNC id not found: {}".format(hgnc_symbol),
'warning')
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
flash("HGNC symbol not found: {}".format(hgnc_symbol),
'warning')
elif is_clinical and (hgnc_symbol not in clinical_symbols):
flash(
"Gene not included in clinical list: {}".format(
hgnc_symbol), 'warning')
else:
hgnc_symbols.append(hgnc_symbol)
form.hgnc_symbols.data = hgnc_symbols
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = {}
if request.args.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
if form.data['chrom'] == 'MT':
# Return all MT variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query)
else:
# Return max 500 variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition',
'attachment',
filename=str(case_obj['_id']) + '-filtered_variants.csv')
return Response(
generate(",".join(document_header), export_lines),
mimetype='text/csv',
headers=headers) # return a csv with the exported variants
else:
data = controllers.variants(store, institute_obj, case_obj,
variants_query, page)
return dict(institute=institute_obj,
case=case_obj,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
def phenotypes_genes(store, case_obj, is_clinical=True):
"""Generate a dictionary consisting of phenotype terms with associated genes from the case HPO panel
Args:
store(adapter.MongoAdapter)
case_obj(dict): models.Case
is_clinical(bool): if True, only list genes from HPO that are among the case clinical_symbols
Returns:
hpo_genes(dict): a dictionary with HPO term IDs as keys and HPO terms and genes as values
If the dynamic phenotype panel is empty, or has been intersected to some level,
use dynamic gene list directly instead.
"""
build = case_obj["genome_build"]
# Make sure build is either "37" or "38"
if "38" in str(build):
build = "38"
else:
build = "37"
dynamic_gene_list = [gene["hgnc_id"] for gene in case_obj.get("dynamic_gene_list", [])]
hpo_genes = {}
clinical_symbols = store.clinical_symbols(case_obj) if is_clinical else None
unique_genes = hpo_genes_from_dynamic_gene_list(case_obj, is_clinical, clinical_symbols)
by_phenotype = True # display genes by phenotype
hpo_gene_list = case_obj.get("dynamic_panel_phenotypes", [])
if not hpo_gene_list and dynamic_gene_list:
by_phenotype = False
all_hpo_gene_list_genes = set()
# Loop over the dynamic phenotypes of a case
for hpo_id in hpo_gene_list:
hpo_term = store.hpo_term(hpo_id)
# Check that HPO term exists in database
if hpo_term is None:
LOG.warning(f"Could not find HPO term with ID '{hpo_id}' in database")
continue
# Create a list with all gene symbols (or HGNC ID if symbol is missing) associated with the phenotype
gene_list = []
for gene_id in hpo_term.get("genes", []):
gene_caption = store.hgnc_gene_caption(gene_id, build)
if gene_caption is None:
continue
if gene_id not in dynamic_gene_list:
# gene was filtered out because min matching phenotypes > 1 (or the panel was generated with older genotype-phenotype mapping)
by_phenotype = False # do not display genes by phenotype
continue
add_symbol = gene_caption.get("hgnc_symbol", f"hgnc:{gene_id}")
if is_clinical and (add_symbol not in clinical_symbols):
continue
gene_list.append(add_symbol)
all_hpo_gene_list_genes.add(add_symbol)
hpo_genes[hpo_id] = {
"description": hpo_term.get("description"),
"genes": ", ".join(sorted(gene_list)),
}
if by_phenotype is True:
# if some gene was manually added (or is left on dynamic panel for other reasons)
non_hpo_genes = unique_genes - all_hpo_gene_list_genes
if len(non_hpo_genes) > 0:
hpo_genes["Analysed genes"] = {
"description": "Non HPO panel genes",
"genes": ", ".join(sorted(non_hpo_genes)),
}
if by_phenotype is False:
hpo_genes = {}
hpo_genes["Analysed genes"] = {
"description": "HPO panel",
"genes": ", ".join(sorted(unique_genes)),
}
return hpo_genes
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.args.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
form = FiltersForm(request.args)
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in case_obj.get('panels', [])]
form.gene_panels.choices = panel_choices
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
if 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:
flash("HGNC id not found: {}".format(hgnc_symbol),
'warning')
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
flash("HGNC symbol not found: {}".format(hgnc_symbol),
'warning')
elif is_clinical and (hgnc_symbol not in clinical_symbols):
flash(
"Gene not included in clinical list: {}".format(
hgnc_symbol), 'warning')
else:
hgnc_symbols.append(hgnc_symbol)
form.hgnc_symbols.data = hgnc_symbols
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = controllers.variants(store, institute_obj, case_obj, variants_query,
page)
return dict(institute=institute_obj,
case=case_obj,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_type = request.args.get('variant_type', 'clinical')
# Update filter settings if Clinical Filter was requested
default_panels = []
for panel in case_obj['panels']:
if panel.get('is_default'):
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type': 'clinical',
'region_annotations': ['exonic','splicing'],
'functional_annotations': SEVERE_SO_TERMS,
'clinsig': [4,5],
'clinsig_confident_always_returned': True,
'gnomad_frequency': str(institute_obj['frequency_cutoff']),
'variant_type': 'clinical',
'gene_panels': default_panels
})
if(request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = FiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = FiltersForm(request.form)
else:
form = FiltersForm(request.args)
# populate available panel choices
available_panels = case_obj.get('panels', []) + [
{'panel_name': 'hpo', 'display_name': 'HPO'}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
# upload gene panel if symbol file exists
if (request.files):
file = request.files[form.symbol_file.name]
if request.files and file and file.filename != '':
log.debug("Upload file request files: {0}".format(request.files.to_dict()))
try:
stream = io.StringIO(file.stream.read().decode('utf-8'), newline=None)
except UnicodeDecodeError as error:
flash("Only text files are supported!", 'warning')
return redirect(request.referrer)
hgnc_symbols_set = set(form.hgnc_symbols.data)
log.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set))
new_hgnc_symbols = controllers.upload_panel(store, institute_id, case_name, stream)
hgnc_symbols_set.update(new_hgnc_symbols)
form.hgnc_symbols.data = hgnc_symbols_set
# reset gene panels
form.gene_panels.data = ''
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case', institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active', case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
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
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(set(term_obj['hgnc_symbol'] for term_obj in
case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = {}
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
if form.data['chrom'] == 'MT':
# Return all MT variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query)
else:
# Return max 500 variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition','attachment', filename=str(case_obj['display_name'])+'-filtered_variants.csv')
# return a csv with the exported variants
return Response(generate(",".join(document_header), export_lines), mimetype='text/csv',
headers=headers)
data = controllers.variants(store, institute_obj, case_obj, variants_query, page)
return dict(institute=institute_obj, case=case_obj, form=form,
severe_so_terms=SEVERE_SO_TERMS, page=page, **data)
def sv_variants(institute_id, case_name):
"""Display a list of structural variants."""
page = int(request.form.get('page', 1))
variant_type = request.args.get('variant_type', 'clinical')
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
form = SvFiltersForm(request.form)
default_panels = []
for panel in case_obj['panels']:
if (panel.get('is_default') and panel['is_default'] is True) or ('default_panels' in case_obj and panel['panel_id'] in case_obj['default_panels']):
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type': 'clinical',
'region_annotations': ['exonic','splicing'],
'functional_annotations': SEVERE_SO_TERMS,
'thousand_genomes_frequency': str(institute_obj['frequency_cutoff']),
'variant_type': 'clinical',
'clingen_ngi': 10,
'swegen': 10,
'size': 100,
'gene_panels': default_panels
})
if(request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = SvFiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = SvFiltersForm(request.form)
else:
form = SvFiltersForm(request.args)
available_panels = case_obj.get('panels', []) + [
{'panel_name': 'hpo', 'display_name': 'HPO'}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
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 sum(1 for i in store.hgnc_genes(hgnc_symbol)) == 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
# handle HPO gene list separately
if 'hpo' in form.data['gene_panels']:
hpo_symbols = list(set(term_obj['hgnc_symbol'] for term_obj in
case_obj['dynamic_gene_list']))
current_symbols = set(hgnc_symbols)
current_symbols.update(hpo_symbols)
form.hgnc_symbols.data = list(current_symbols)
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case', institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active', case_link)
variants_query = store.variants(case_obj['_id'], category='sv',
query=form.data)
data = {}
# if variants should be exported
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
# Return max 500 variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition','attachment', filename=str(case_obj['display_name'])+'-filtered_sv-variants.csv')
return Response(generate(",".join(document_header), export_lines), mimetype='text/csv', headers=headers) # return a csv with the exported variants
else:
data = controllers.sv_variants(store, institute_obj, case_obj,
variants_query, page)
return dict(institute=institute_obj, case=case_obj, variant_type=variant_type,
form=form, severe_so_terms=SEVERE_SO_TERMS, page=page, **data)