_id stringlengths 2 7 | title stringlengths 1 88 | partition stringclasses 3
values | text stringlengths 75 19.8k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q273400 | build_clnsig | test | def build_clnsig(clnsig_info):
"""docstring for build_clnsig"""
clnsig_obj = dict(
value = clnsig_info['value'],
accession = clnsig_info.get('accession'),
revstat = clnsig_info.get('revstat')
)
return clnsig_obj | python | {
"resource": ""
} |
q273401 | GeneHandler.load_hgnc_bulk | test | def load_hgnc_bulk(self, gene_objs):
"""Load a bulk of hgnc gene objects
Raises IntegrityError if there are any write concerns
Args:
gene_objs(iterable(scout.models.hgnc_gene))
Returns:
result (pymongo.results.InsertManyResult)
"""
LOG.... | python | {
"resource": ""
} |
q273402 | GeneHandler.load_transcript_bulk | test | def load_transcript_bulk(self, transcript_objs):
"""Load a bulk of transcript objects to the database
Arguments:
transcript_objs(iterable(scout.models.hgnc_transcript))
"""
LOG.info("Loading transcript bulk")
try:
result = self.transcript_collection.inse... | python | {
"resource": ""
} |
q273403 | GeneHandler.load_exon_bulk | test | def load_exon_bulk(self, exon_objs):
"""Load a bulk of exon objects to the database
Arguments:
exon_objs(iterable(scout.models.hgnc_exon))
"""
try:
result = self.exon_collection.insert_many(transcript_objs)
except (DuplicateKeyError, BulkWriteError) as e... | python | {
"resource": ""
} |
q273404 | GeneHandler.hgnc_gene | test | def hgnc_gene(self, hgnc_identifier, build='37'):
"""Fetch a hgnc gene
Args:
hgnc_identifier(int)
Returns:
gene_obj(HgncGene)
"""
if not build in ['37', '38']:
build = '37'
query = {}
try:
# If the ... | python | {
"resource": ""
} |
q273405 | GeneHandler.hgnc_id | test | def hgnc_id(self, hgnc_symbol, build='37'):
"""Query the genes with a hgnc symbol and return the hgnc id
Args:
hgnc_symbol(str)
build(str)
Returns:
hgnc_id(int)
"""
#LOG.debug("Fetching gene %s", hgnc_symbol)
query = {'hgnc_symbol':hg... | python | {
"resource": ""
} |
q273406 | GeneHandler.hgnc_genes | test | def hgnc_genes(self, hgnc_symbol, build='37', search=False):
"""Fetch all hgnc genes that match a hgnc symbol
Check both hgnc_symbol and aliases
Args:
hgnc_symbol(str)
build(str): The build in which to search
search(bool): if partial sear... | python | {
"resource": ""
} |
q273407 | GeneHandler.all_genes | test | def all_genes(self, build='37'):
"""Fetch all hgnc genes
Returns:
result()
"""
LOG.info("Fetching all genes")
return self.hgnc_collection.find({'build': build}).sort('chromosome', 1) | python | {
"resource": ""
} |
q273408 | GeneHandler.nr_genes | test | def nr_genes(self, build=None):
"""Return the number of hgnc genes in collection
If build is used, return the number of genes of a certain build
Returns:
result()
"""
if build:
LOG.info("Fetching all genes from build %s", build)
else:
... | python | {
"resource": ""
} |
q273409 | GeneHandler.drop_genes | test | def drop_genes(self, build=None):
"""Delete the genes collection"""
if build:
LOG.info("Dropping the hgnc_gene collection, build %s", build)
self.hgnc_collection.delete_many({'build': build})
else:
LOG.info("Dropping the hgnc_gene collection")
self... | python | {
"resource": ""
} |
q273410 | GeneHandler.drop_transcripts | test | def drop_transcripts(self, build=None):
"""Delete the transcripts collection"""
if build:
LOG.info("Dropping the transcripts collection, build %s", build)
self.transcript_collection.delete_many({'build': build})
else:
LOG.info("Dropping the transcripts collect... | python | {
"resource": ""
} |
q273411 | GeneHandler.drop_exons | test | def drop_exons(self, build=None):
"""Delete the exons collection"""
if build:
LOG.info("Dropping the exons collection, build %s", build)
self.exon_collection.delete_many({'build': build})
else:
LOG.info("Dropping the exons collection")
self.exon_co... | python | {
"resource": ""
} |
q273412 | GeneHandler.ensembl_transcripts | test | def ensembl_transcripts(self, build='37'):
"""Return a dictionary with ensembl ids as keys and transcripts as value.
Args:
build(str)
Returns:
ensembl_transcripts(dict): {<enst_id>: transcripts_obj, ...}
"""
ensembl_transcripts = {}
LOG.i... | python | {
"resource": ""
} |
q273413 | GeneHandler.hgncsymbol_to_gene | test | def hgncsymbol_to_gene(self, build='37', genes=None):
"""Return a dictionary with hgnc_symbol as key and gene_obj as value
The result will have ONE entry for each gene in the database.
(For a specific build)
Args:
build(str)
genes(iterable(scout.models.HgncGene)... | python | {
"resource": ""
} |
q273414 | GeneHandler.gene_by_alias | test | def gene_by_alias(self, symbol, build='37'):
"""Return a iterable with hgnc_genes.
If the gene symbol is listed as primary the iterable will only have
one result. If not the iterable will include all hgnc genes that have
the symbol as an alias.
Args:
symbol(str)
... | python | {
"resource": ""
} |
q273415 | GeneHandler.genes_by_alias | test | def genes_by_alias(self, build='37', genes=None):
"""Return a dictionary with hgnc symbols as keys and a list of hgnc ids
as value.
If a gene symbol is listed as primary the list of ids will only consist
of that entry if not the gene can not be determined so the result is a list
... | python | {
"resource": ""
} |
q273416 | GeneHandler.ensembl_genes | test | def ensembl_genes(self, build='37'):
"""Return a dictionary with ensembl ids as keys and gene objects as value.
Args:
build(str)
Returns:
genes(dict): {<ensg_id>: gene_obj, ...}
"""
genes = {}
LOG.info("Fetching all genes")
... | python | {
"resource": ""
} |
q273417 | GeneHandler.to_hgnc | test | def to_hgnc(self, hgnc_alias, build='37'):
"""Check if a hgnc symbol is an alias
Return the correct hgnc symbol, if not existing return None
Args:
hgnc_alias(str)
Returns:
hgnc_symbol(str)
"""
result = self.hgnc_genes(hgnc_sy... | python | {
"resource": ""
} |
q273418 | GeneHandler.add_hgnc_id | test | def add_hgnc_id(self, genes):
"""Add the correct hgnc id to a set of genes with hgnc symbols
Args:
genes(list(dict)): A set of genes with hgnc symbols only
"""
genes_by_alias = self.genes_by_alias()
for gene in genes:
id_info = genes_by_alias.get(gene['... | python | {
"resource": ""
} |
q273419 | GeneHandler.get_coding_intervals | test | def get_coding_intervals(self, build='37', genes=None):
"""Return a dictionary with chromosomes as keys and interval trees as values
Each interval represents a coding region of overlapping genes.
Args:
build(str): The genome build
genes(iterable(scout.models.HgncGene)):... | python | {
"resource": ""
} |
q273420 | omim | test | def omim(context, api_key, institute):
"""
Update the automate generated omim gene panel in the database.
"""
LOG.info("Running scout update omim")
adapter = context.obj['adapter']
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a... | python | {
"resource": ""
} |
q273421 | cases | test | def cases(institute_id):
"""Display a list of cases for an institute."""
institute_obj = institute_and_case(store, institute_id)
query = request.args.get('query')
limit = 100
if request.args.get('limit'):
limit = int(request.args.get('limit'))
skip_assigned = request.args.get('skip_ass... | python | {
"resource": ""
} |
q273422 | case | test | def case(institute_id, case_name):
"""Display one case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
data = controllers.case(store, institute_obj, case_obj)
return dict(institute=institute_obj, case=case_obj, **data) | python | {
"resource": ""
} |
q273423 | matchmaker_matches | test | def matchmaker_matches(institute_id, case_name):
"""Show all MatchMaker matches for a given case"""
# check that only authorized users can access MME patients matches
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
... | python | {
"resource": ""
} |
q273424 | matchmaker_match | test | def matchmaker_match(institute_id, case_name, target):
"""Starts an internal match or a match against one or all MME external nodes"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
# check that only authorized users can run matches
user_obj = store.user(current_user.email... | python | {
"resource": ""
} |
q273425 | matchmaker_delete | test | def matchmaker_delete(institute_id, case_name):
"""Remove a case from MatchMaker"""
# check that only authorized users can delete patients from MME
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redi... | python | {
"resource": ""
} |
q273426 | case_report | test | def case_report(institute_id, case_name):
"""Visualize case report"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
data = controllers.case_report_content(store, institute_obj, case_obj)
return dict(institute=institute_obj, case=case_obj, format='html', **data) | python | {
"resource": ""
} |
q273427 | pdf_case_report | test | def pdf_case_report(institute_id, case_name):
"""Download a pdf report for a case"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
data = controllers.case_report_content(store, institute_obj, case_obj)
# add coverage report on the bottom of this report
if current_app... | python | {
"resource": ""
} |
q273428 | case_diagnosis | test | def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
level = 'phenotype' ... | python | {
"resource": ""
} |
q273429 | phenotypes | test | def phenotypes(institute_id, case_name, phenotype_id=None):
"""Handle phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
is_group = request.args.get('is_group') == 'yes'
user_obj = st... | python | {
"resource": ""
} |
q273430 | phenotypes_actions | test | def phenotypes_actions(institute_id, case_name):
"""Perform actions on multiple phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
action = request.form['action']
hpo_ids = request.fo... | python | {
"resource": ""
} |
q273431 | events | test | def events(institute_id, case_name, event_id=None):
"""Handle events."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = request.form.get('link')
content = request.form.get('content')
variant_id = request.args.get('variant_id')
user_obj = store.user(current_us... | python | {
"resource": ""
} |
q273432 | status | test | def status(institute_id, case_name):
"""Update status of a specific case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
status = request.form.get('status', case_obj['status'])
link = url_for('.case', institute_id=institute_... | python | {
"resource": ""
} |
q273433 | assign | test | def assign(institute_id, case_name, user_id=None):
"""Assign and unassign a user from a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if user_id:
user_obj = store.user(user_id)
els... | python | {
"resource": ""
} |
q273434 | hpoterms | test | def hpoterms():
"""Search for HPO terms."""
query = request.args.get('query')
if query is None:
return abort(500)
terms = sorted(store.hpo_terms(query=query), key=itemgetter('hpo_number'))
json_terms = [
{'name': '{} | {}'.format(term['_id'], term['description']),
'id': term... | python | {
"resource": ""
} |
q273435 | mark_validation | test | def mark_validation(institute_id, case_name, variant_id):
"""Mark a variant as sanger validated."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
validate_type = request.form['type'] or N... | python | {
"resource": ""
} |
q273436 | mark_causative | test | def mark_causative(institute_id, case_name, variant_id):
"""Mark a variant as confirmed causative."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', inst... | python | {
"resource": ""
} |
q273437 | delivery_report | test | def delivery_report(institute_id, case_name):
"""Display delivery report."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
if case_obj.get('delivery_report') is None:
return abort(404)
date_str = request.args.get('date')
if date_str:
delivery_report = ... | python | {
"resource": ""
} |
q273438 | share | test | def share(institute_id, case_name):
"""Share a case with a different institute."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
collaborator_id = request.form['collaborator']
revoke_access = 'revoke' in request.form
link =... | python | {
"resource": ""
} |
q273439 | rerun | test | def rerun(institute_id, case_name):
"""Request a case to be rerun."""
sender = current_app.config['MAIL_USERNAME']
recipient = current_app.config['TICKET_SYSTEM_EMAIL']
controllers.rerun(store, mail, current_user, institute_id, case_name, sender,
recipient)
return redirect(requ... | python | {
"resource": ""
} |
q273440 | research | test | def research(institute_id, case_name):
"""Open the research list for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
store.open_research(institute... | python | {
"resource": ""
} |
q273441 | vcf2cytosure | test | def vcf2cytosure(institute_id, case_name, individual_id):
"""Download vcf2cytosure file for individual."""
(display_name, vcf2cytosure) = controllers.vcf2cytosure(store,
institute_id, case_name, individual_id)
outdir = os.path.abspath(os.path.dirname(vcf2cytosure))
filename = os.path.basename(... | python | {
"resource": ""
} |
q273442 | multiqc | test | def multiqc(institute_id, case_name):
"""Load multiqc report for the case."""
data = controllers.multiqc(store, institute_id, case_name)
if data['case'].get('multiqc') is None:
return abort(404)
out_dir = os.path.abspath(os.path.dirname(data['case']['multiqc']))
filename = os.path.basename(d... | python | {
"resource": ""
} |
q273443 | cases | test | def cases(store, case_query, limit=100):
"""Preprocess case objects.
Add the necessary information to display the 'cases' view
Args:
store(adapter.MongoAdapter)
case_query(pymongo.Cursor)
limit(int): Maximum number of cases to display
Returns:
data(dict): includes the ... | python | {
"resource": ""
} |
q273444 | case_report_content | test | def case_report_content(store, institute_obj, case_obj):
"""Gather contents to be visualized in a case report
Args:
store(adapter.MongoAdapter)
institute_obj(models.Institute)
case_obj(models.Case)
Returns:
data(dict)
"""
variant_types = {
'causatives_detai... | python | {
"resource": ""
} |
q273445 | coverage_report_contents | test | def coverage_report_contents(store, institute_obj, case_obj, base_url):
"""Posts a request to chanjo-report and capture the body of the returned response to include it in case report
Args:
store(adapter.MongoAdapter)
institute_obj(models.Institute)
case_obj(models.Case)
base_url... | python | {
"resource": ""
} |
q273446 | clinvar_submissions | test | def clinvar_submissions(store, user_id, institute_id):
"""Get all Clinvar submissions for a user and an institute"""
submissions = list(store.clinvar_submissions(user_id, institute_id))
return submissions | python | {
"resource": ""
} |
q273447 | mt_excel_files | test | def mt_excel_files(store, case_obj, temp_excel_dir):
"""Collect MT variants and format line of a MT variant report
to be exported in excel format
Args:
store(adapter.MongoAdapter)
case_obj(models.Case)
temp_excel_dir(os.Path): folder where the temp excel files are written to
Re... | python | {
"resource": ""
} |
q273448 | update_synopsis | test | def update_synopsis(store, institute_obj, case_obj, user_obj, new_synopsis):
"""Update synopsis."""
# create event only if synopsis was actually changed
if case_obj['synopsis'] != new_synopsis:
link = url_for('cases.case', institute_id=institute_obj['_id'],
case_name=case_obj[... | python | {
"resource": ""
} |
q273449 | hpo_diseases | test | def hpo_diseases(username, password, hpo_ids, p_value_treshold=1):
"""Return the list of HGNC symbols that match annotated HPO terms.
Args:
username (str): username to use for phenomizer connection
password (str): password to use for phenomizer connection
Returns:
query_result: a g... | python | {
"resource": ""
} |
q273450 | vcf2cytosure | test | def vcf2cytosure(store, institute_id, case_name, individual_id):
"""vcf2cytosure CGH file for inidividual."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
for individual in case_obj['individuals']:
if individual['individual_id'] == individual_id:
individu... | python | {
"resource": ""
} |
q273451 | multiqc | test | def multiqc(store, institute_id, case_name):
"""Find MultiQC report for the case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
return dict(
institute=institute_obj,
case=case_obj,
) | python | {
"resource": ""
} |
q273452 | get_sanger_unevaluated | test | def get_sanger_unevaluated(store, institute_id, user_id):
"""Get all variants for an institute having Sanger validations ordered but still not evaluated
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
Returns:
unevaluated: a list that looks like this: ... | python | {
"resource": ""
} |
q273453 | mme_add | test | def mme_add(store, user_obj, case_obj, add_gender, add_features, add_disorders, genes_only,
mme_base_url, mme_accepts, mme_token):
"""Add a patient to MatchMaker server
Args:
store(adapter.MongoAdapter)
user_obj(dict) a scout user object (to be added as matchmaker contact)
case_obj(... | python | {
"resource": ""
} |
q273454 | mme_delete | test | def mme_delete(case_obj, mme_base_url, mme_token):
"""Delete all affected samples for a case from MatchMaker
Args:
case_obj(dict) a scout case object
mme_base_url(str) base url of the MME server
mme_token(str) auth token of the MME server
Returns:
server_responses(list): a... | python | {
"resource": ""
} |
q273455 | mme_matches | test | def mme_matches(case_obj, institute_obj, mme_base_url, mme_token):
"""Show Matchmaker submission data for a sample and eventual matches.
Args:
case_obj(dict): a scout case object
institute_obj(dict): an institute object
mme_base_url(str) base url of the MME server
mme_token(str)... | python | {
"resource": ""
} |
q273456 | mme_match | test | def mme_match(case_obj, match_type, mme_base_url, mme_token, nodes=None, mme_accepts=None):
"""Initiate a MatchMaker match against either other Scout patients or external nodes
Args:
case_obj(dict): a scout case object already submitted to MME
match_type(str): 'internal' or 'external'
m... | python | {
"resource": ""
} |
q273457 | genes | test | 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 ... | python | {
"resource": ""
} |
q273458 | parse_callers | test | def parse_callers(variant, category='snv'):
"""Parse how the different variant callers have performed
Args:
variant (cyvcf2.Variant): A variant object
Returns:
callers (dict): A dictionary on the format
{'gatk': <filter>,'freebayes': <filter>,'samtools': <filter... | python | {
"resource": ""
} |
q273459 | build_transcript | test | def build_transcript(transcript_info, build='37'):
"""Build a hgnc_transcript object
Args:
transcript_info(dict): Transcript information
Returns:
transcript_obj(HgncTranscript)
{
transcript_id: str, required
hgnc_id: int, required... | python | {
"resource": ""
} |
q273460 | load_institute | test | def load_institute(adapter, internal_id, display_name, sanger_recipients=None):
"""Load a institute into the database
Args:
adapter(MongoAdapter)
internal_id(str)
display_name(str)
sanger_recipients(list(email))
"""
institute_obj = build_institute(
... | python | {
"resource": ""
} |
q273461 | parse_cadd | test | def parse_cadd(variant, transcripts):
"""Check if the cadd phred score is annotated"""
cadd = 0
cadd_keys = ['CADD', 'CADD_PHRED']
for key in cadd_keys:
cadd = variant.INFO.get(key, 0)
if cadd:
return float(cadd)
for transcript in transcripts:
cadd_entry = tr... | python | {
"resource": ""
} |
q273462 | case | test | def case(context, vcf, vcf_sv, vcf_cancer, vcf_str, owner, ped, update, config,
no_variants, peddy_ped, peddy_sex, peddy_check):
"""Load a case into the database.
A case can be loaded without specifying vcf files and/or bam files
"""
adapter = context.obj['adapter']
if config is None and ... | python | {
"resource": ""
} |
q273463 | VariantLoader.update_variant | test | def update_variant(self, variant_obj):
"""Update one variant document in the database.
This means that the variant in the database will be replaced by variant_obj.
Args:
variant_obj(dict)
Returns:
new_variant(dict)
"""
LOG.debug('Updating varian... | python | {
"resource": ""
} |
q273464 | VariantLoader.update_variant_rank | test | def update_variant_rank(self, case_obj, variant_type='clinical', category='snv'):
"""Updates the manual rank for all variants in a case
Add a variant rank based on the rank score
Whenever variants are added or removed from a case we need to update the variant rank
Args:
cas... | python | {
"resource": ""
} |
q273465 | VariantLoader.update_variant_compounds | test | def update_variant_compounds(self, variant, variant_objs = None):
"""Update compounds for a variant.
This will add all the necessary information of a variant on a compound object.
Args:
variant(scout.models.Variant)
variant_objs(dict): A dictionary with _ids as keys and... | python | {
"resource": ""
} |
q273466 | VariantLoader.update_compounds | test | def update_compounds(self, variants):
"""Update the compounds for a set of variants.
Args:
variants(dict): A dictionary with _ids as keys and variant objs as values
"""
LOG.debug("Updating compound objects")
for var_id in variants:
variant_obj = variant... | python | {
"resource": ""
} |
q273467 | VariantLoader.update_mongo_compound_variants | test | def update_mongo_compound_variants(self, bulk):
"""Update the compound information for a bulk of variants in the database
Args:
bulk(dict): {'_id': scout.models.Variant}
"""
requests = []
for var_id in bulk:
var_obj = bulk[var_id]
if ... | python | {
"resource": ""
} |
q273468 | VariantLoader.update_case_compounds | test | def update_case_compounds(self, case_obj, build='37'):
"""Update the compounds for a case
Loop over all coding intervals to get coordinates for all potential compound positions.
Update all variants within a gene with a bulk operation.
"""
case_id = case_obj['_id']
# Pos... | python | {
"resource": ""
} |
q273469 | VariantLoader.load_variant | test | def load_variant(self, variant_obj):
"""Load a variant object
Args:
variant_obj(dict)
Returns:
inserted_id
"""
# LOG.debug("Loading variant %s", variant_obj['_id'])
try:
result = self.variant_collection.insert_one(variant_obj)
... | python | {
"resource": ""
} |
q273470 | VariantLoader.upsert_variant | test | def upsert_variant(self, variant_obj):
"""Load a variant object, if the object already exists update compounds.
Args:
variant_obj(dict)
Returns:
result
"""
LOG.debug("Upserting variant %s", variant_obj['_id'])
try:
result = self.varia... | python | {
"resource": ""
} |
q273471 | VariantLoader.load_variant_bulk | test | def load_variant_bulk(self, variants):
"""Load a bulk of variants
Args:
variants(iterable(scout.models.Variant))
Returns:
object_ids
"""
if not len(variants) > 0:
return
LOG.debug("Loading variant bulk")
try:
resu... | python | {
"resource": ""
} |
q273472 | CaseEventHandler.assign | test | def assign(self, institute, case, user, link):
"""Assign a user to a case.
This function will create an Event to log that a person has been assigned
to a case. Also the user will be added to case "assignees".
Arguments:
institute (dict): A institute
case (dict):... | python | {
"resource": ""
} |
q273473 | CaseEventHandler.share | test | def share(self, institute, case, collaborator_id, user, link):
"""Share a case with a new institute.
Arguments:
institute (dict): A Institute object
case (dict): Case object
collaborator_id (str): A instute id
user (dict): A User object
link (... | python | {
"resource": ""
} |
q273474 | CaseEventHandler.diagnose | test | def diagnose(self, institute, case, user, link, level, omim_id, remove=False):
"""Diagnose a case using OMIM ids.
Arguments:
institute (dict): A Institute object
case (dict): Case object
user (dict): A User object
link (str): The url to be used in the eve... | python | {
"resource": ""
} |
q273475 | CaseEventHandler.mark_checked | test | def mark_checked(self, institute, case, user, link,
unmark=False):
"""Mark a case as checked from an analysis point of view.
Arguments:
institute (dict): A Institute object
case (dict): Case object
user (dict): A User object
link (str... | python | {
"resource": ""
} |
q273476 | VariantEventHandler.order_verification | test | def order_verification(self, institute, case, user, link, variant):
"""Create an event for a variant verification for a variant
and an event for a variant verification for a case
Arguments:
institute (dict): A Institute object
case (dict): Case object
user (d... | python | {
"resource": ""
} |
q273477 | VariantEventHandler.sanger_ordered | test | def sanger_ordered(self, institute_id=None, user_id=None):
"""Get all variants with validations ever ordered.
Args:
institute_id(str) : The id of an institute
user_id(str) : The id of an user
Returns:
sanger_ordered(list) : a list of dictionaries, each with ... | python | {
"resource": ""
} |
q273478 | VariantEventHandler.validate | test | def validate(self, institute, case, user, link, variant, validate_type):
"""Mark validation status for a variant.
Arguments:
institute (dict): A Institute object
case (dict): Case object
user (dict): A User object
link (str): The url to be used in the eve... | python | {
"resource": ""
} |
q273479 | VariantEventHandler.mark_causative | test | def mark_causative(self, institute, case, user, link, variant):
"""Create an event for marking a variant causative.
Arguments:
institute (dict): A Institute object
case (dict): Case object
user (dict): A User object
link (str): The url to be used in the event
... | python | {
"resource": ""
} |
q273480 | VariantEventHandler.update_dismiss_variant | test | def update_dismiss_variant(self, institute, case, user, link, variant,
dismiss_variant):
"""Create an event for updating the manual dismiss variant entry
This function will create a event and update the dismiss variant
field of the variant.
Arguments:... | python | {
"resource": ""
} |
q273481 | VariantEventHandler.update_acmg | test | def update_acmg(self, institute_obj, case_obj, user_obj, link, variant_obj, acmg_str):
"""Create an event for updating the ACMG classification of a variant.
Arguments:
institute_obj (dict): A Institute object
case_obj (dict): Case object
user_obj (dict): A User objec... | python | {
"resource": ""
} |
q273482 | parse_ids | test | def parse_ids(chrom, pos, ref, alt, case_id, variant_type):
"""Construct the necessary ids for a variant
Args:
chrom(str): Variant chromosome
pos(int): Variant position
ref(str): Variant reference
alt(str): Variant alternative
case_id(str): Unique case id
variant... | python | {
"resource": ""
} |
q273483 | parse_simple_id | test | def parse_simple_id(chrom, pos, ref, alt):
"""Parse the simple id for a variant
Simple id is used as a human readable reference for a position, it is
in no way unique.
Args:
chrom(str)
pos(str)
ref(str)
alt(str)
Returns:
simple_id(str): The simple human rea... | python | {
"resource": ""
} |
q273484 | parse_document_id | test | def parse_document_id(chrom, pos, ref, alt, variant_type, case_id):
"""Parse the unique document id for a variant.
This will always be unique in the database.
Args:
chrom(str)
pos(str)
ref(str)
alt(str)
variant_type(str): 'clinical' or 'research'
case_id(str... | python | {
"resource": ""
} |
q273485 | convert | test | def convert(context, panel):
"""Convert a gene panel with hgnc symbols to a new one with hgnc ids."""
adapter = context.obj['adapter']
new_header = ["hgnc_id","hgnc_symbol","disease_associated_transcripts",
"reduced_penetrance", "genetic_disease_models", "mosaicism",
"datab... | python | {
"resource": ""
} |
q273486 | get_variantid | test | def get_variantid(variant_obj, family_id):
"""Create a new variant id.
Args:
variant_obj(dict)
family_id(str)
Returns:
new_id(str): The new variant id
"""
new_id = parse_document_id(
chrom=variant_obj['chromosome'],
pos=str(variant_obj['position']),
... | python | {
"resource": ""
} |
q273487 | CaseHandler.nr_cases | test | def nr_cases(self, institute_id=None):
"""Return the number of cases
This function will change when we migrate to 3.7.1
Args:
collaborator(str): Institute id
Returns:
nr_cases(int)
"""
query = {}
if institute_id:
query['coll... | python | {
"resource": ""
} |
q273488 | CaseHandler.update_dynamic_gene_list | test | def update_dynamic_gene_list(self, case, hgnc_symbols=None, hgnc_ids=None,
phenotype_ids=None, build='37'):
"""Update the dynamic gene list for a case
Adds a list of dictionaries to case['dynamic_gene_list'] that looks like
{
hgnc_symbol: str,
... | python | {
"resource": ""
} |
q273489 | CaseHandler.case | test | def case(self, case_id=None, institute_id=None, display_name=None):
"""Fetches a single case from database
Use either the _id or combination of institute_id and display_name
Args:
case_id(str): _id for a caes
institute_id(str):
display_name(str)
Yie... | python | {
"resource": ""
} |
q273490 | CaseHandler.delete_case | test | def delete_case(self, case_id=None, institute_id=None, display_name=None):
"""Delete a single case from database
Args:
institute_id(str)
case_id(str)
Returns:
case_obj(dict): The case that was deleted
"""
query = {}
if case_id:
... | python | {
"resource": ""
} |
q273491 | CaseHandler._add_case | test | def _add_case(self, case_obj):
"""Add a case to the database
If the case already exists exception is raised
Args:
case_obj(Case)
"""
if self.case(case_obj['_id']):
raise IntegrityError("Case %s already exists in database" % case_obj['_id'])
... | python | {
"resource": ""
} |
q273492 | CaseHandler.replace_case | test | def replace_case(self, case_obj):
"""Replace a existing case with a new one
Keeps the object id
Args:
case_obj(dict)
Returns:
updated_case(dict)
"""
# Todo: Figure out and describe when this method destroys a case if invoked instead of
#... | python | {
"resource": ""
} |
q273493 | CaseHandler.update_caseid | test | def update_caseid(self, case_obj, family_id):
"""Update case id for a case across the database.
This function is used when a case is a rerun or updated for another reason.
Args:
case_obj(dict)
family_id(str): The new family id
Returns:
new_case(dict... | python | {
"resource": ""
} |
q273494 | ACMGHandler.submit_evaluation | test | def submit_evaluation(self, variant_obj, user_obj, institute_obj, case_obj, link, criteria):
"""Submit an evaluation to the database
Get all the relevant information, build a evaluation_obj
Args:
variant_obj(dict)
user_obj(dict)
institute_obj(dict)
... | python | {
"resource": ""
} |
q273495 | ACMGHandler.get_evaluations | test | def get_evaluations(self, variant_obj):
"""Return all evaluations for a certain variant.
Args:
variant_obj (dict): variant dict from the database
Returns:
pymongo.cursor: database cursor
"""
query = dict(variant_id=variant_obj['variant_id'])
res ... | python | {
"resource": ""
} |
q273496 | parse_transcripts | test | def parse_transcripts(transcript_lines):
"""Parse and massage the transcript information
There could be multiple lines with information about the same transcript.
This is why it is necessary to parse the transcripts first and then return a dictionary
where all information has been merged.
Args:
... | python | {
"resource": ""
} |
q273497 | parse_ensembl_gene_request | test | def parse_ensembl_gene_request(result):
"""Parse a dataframe with ensembl gene information
Args:
res(pandas.DataFrame)
Yields:
gene_info(dict)
"""
LOG.info("Parsing genes from request")
for index, row in result.iterrows():
# print(index, row)
ensembl_info = {}
... | python | {
"resource": ""
} |
q273498 | parse_ensembl_transcript_request | test | def parse_ensembl_transcript_request(result):
"""Parse a dataframe with ensembl transcript information
Args:
res(pandas.DataFrame)
Yields:
transcript_info(dict)
"""
LOG.info("Parsing transcripts from request")
keys = [
'chrom',
'ensembl_gene_id',
'ensem... | python | {
"resource": ""
} |
q273499 | parse_ensembl_line | test | def parse_ensembl_line(line, header):
"""Parse an ensembl formated line
Args:
line(list): A list with ensembl gene info
header(list): A list with the header info
Returns:
ensembl_info(dict): A dictionary with the relevant info
"""
line = line.rstrip().sp... | python | {
"resource": ""
} |
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