_id stringlengths 2 7 | title stringlengths 1 88 | partition stringclasses 3
values | text stringlengths 75 19.8k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q273200 | find_bai_file | test | def find_bai_file(bam_file):
"""Find out BAI file by extension given the BAM file."""
bai_file = bam_file.replace('.bam', '.bai')
if not os.path.exists(bai_file):
# try the other convention
bai_file = "{}.bai".format(bam_file)
return bai_file | python | {
"resource": ""
} |
q273201 | observations | test | def observations(store, loqusdb, case_obj, variant_obj):
"""Query observations for a variant."""
composite_id = ("{this[chromosome]}_{this[position]}_{this[reference]}_"
"{this[alternative]}".format(this=variant_obj))
obs_data = loqusdb.get_variant({'_id': composite_id}) or {}
obs_da... | python | {
"resource": ""
} |
q273202 | parse_gene | test | def parse_gene(gene_obj, build=None):
"""Parse variant genes."""
build = build or 37
if gene_obj.get('common'):
add_gene_links(gene_obj, build)
refseq_transcripts = []
for tx_obj in gene_obj['transcripts']:
parse_transcript(gene_obj, tx_obj, build)
# select ... | python | {
"resource": ""
} |
q273203 | transcript_str | test | def transcript_str(transcript_obj, gene_name=None):
"""Generate amino acid change as a string."""
if transcript_obj.get('exon'):
gene_part, part_count_raw = 'exon', transcript_obj['exon']
elif transcript_obj.get('intron'):
gene_part, part_count_raw = 'intron', transcript_obj['intron']
el... | python | {
"resource": ""
} |
q273204 | end_position | test | def end_position(variant_obj):
"""Calculate end position for a variant."""
alt_bases = len(variant_obj['alternative'])
num_bases = max(len(variant_obj['reference']), alt_bases)
return variant_obj['position'] + (num_bases - 1) | python | {
"resource": ""
} |
q273205 | frequency | test | def frequency(variant_obj):
"""Returns a judgement on the overall frequency of the variant.
Combines multiple metrics into a single call.
"""
most_common_frequency = max(variant_obj.get('thousand_genomes_frequency') or 0,
variant_obj.get('exac_frequency') or 0)
if mo... | python | {
"resource": ""
} |
q273206 | clinsig_human | test | def clinsig_human(variant_obj):
"""Convert to human readable version of CLINSIG evaluation."""
for clinsig_obj in variant_obj['clnsig']:
# The clinsig objects allways have a accession
if isinstance(clinsig_obj['accession'], int):
# New version
link = "https://www.ncbi.nlm... | python | {
"resource": ""
} |
q273207 | thousandg_link | test | def thousandg_link(variant_obj, build=None):
"""Compose link to 1000G page for detailed information."""
dbsnp_id = variant_obj.get('dbsnp_id')
build = build or 37
if not dbsnp_id:
return None
if build == 37:
url_template = ("http://grch37.ensembl.org/Homo_sapiens/Variation/Explore"... | python | {
"resource": ""
} |
q273208 | cosmic_link | test | def cosmic_link(variant_obj):
"""Compose link to COSMIC Database.
Args:
variant_obj(scout.models.Variant)
Returns:
url_template(str): Link to COSMIIC database if cosmic id is present
"""
cosmic_ids = variant_obj.get('cosmic_ids')
if not cosmic_ids:
return None
els... | python | {
"resource": ""
} |
q273209 | beacon_link | test | def beacon_link(variant_obj, build=None):
"""Compose link to Beacon Network."""
build = build or 37
url_template = ("https://beacon-network.org/#/search?pos={this[position]}&"
"chrom={this[chromosome]}&allele={this[alternative]}&"
"ref={this[reference]}&rs=GRCh37")
... | python | {
"resource": ""
} |
q273210 | ucsc_link | test | def ucsc_link(variant_obj, build=None):
"""Compose link to UCSC."""
build = build or 37
url_template = ("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&"
"position=chr{this[chromosome]}:{this[position]}"
"-{this[position]}&dgv=pack&knownGene=pack&omimGene=pac... | python | {
"resource": ""
} |
q273211 | spidex_human | test | def spidex_human(variant_obj):
"""Translate SPIDEX annotation to human readable string."""
if variant_obj.get('spidex') is None:
return 'not_reported'
elif abs(variant_obj['spidex']) < SPIDEX_HUMAN['low']['pos'][1]:
return 'low'
elif abs(variant_obj['spidex']) < SPIDEX_HUMAN['medium']['p... | python | {
"resource": ""
} |
q273212 | expected_inheritance | test | def expected_inheritance(variant_obj):
"""Gather information from common gene information."""
manual_models = set()
for gene in variant_obj.get('genes', []):
manual_models.update(gene.get('manual_inheritance', []))
return list(manual_models) | python | {
"resource": ""
} |
q273213 | callers | test | def callers(variant_obj, category='snv'):
"""Return info about callers."""
calls = set()
for caller in CALLERS[category]:
if variant_obj.get(caller['id']):
calls.add((caller['name'], variant_obj[caller['id']]))
return list(calls) | python | {
"resource": ""
} |
q273214 | cancer_variants | test | def cancer_variants(store, request_args, institute_id, case_name):
"""Fetch data related to cancer variants for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
form = CancerFiltersForm(request_args)
variants_query = store.variants(case_obj['_id'], category='cancer... | python | {
"resource": ""
} |
q273215 | clinvar_export | test | def clinvar_export(store, institute_id, case_name, variant_id):
"""Gather the required data for creating the clinvar submission form
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): case ID
variant_id(str): variant._id
... | python | {
"resource": ""
} |
q273216 | get_clinvar_submission | test | def get_clinvar_submission(store, institute_id, case_name, variant_id, submission_id):
"""Collects all variants from the clinvar submission collection with a specific submission_id
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): ca... | python | {
"resource": ""
} |
q273217 | variant_acmg | test | def variant_acmg(store, institute_id, case_name, variant_id):
"""Collect data relevant for rendering ACMG classification form."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
return dict(institute=institute_obj, case=case_obj, varia... | python | {
"resource": ""
} |
q273218 | variant_acmg_post | test | def variant_acmg_post(store, institute_id, case_name, variant_id, user_email, criteria):
"""Calculate an ACMG classification based on a list of criteria."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(user_ema... | python | {
"resource": ""
} |
q273219 | evaluation | test | def evaluation(store, evaluation_obj):
"""Fetch and fill-in evaluation object."""
evaluation_obj['institute'] = store.institute(evaluation_obj['institute_id'])
evaluation_obj['case'] = store.case(evaluation_obj['case_id'])
evaluation_obj['variant'] = store.variant(evaluation_obj['variant_specific'])
... | python | {
"resource": ""
} |
q273220 | upload_panel | test | def upload_panel(store, institute_id, case_name, stream):
"""Parse out HGNC symbols from a stream."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
raw_symbols = [line.strip().split('\t')[0] for line in stream if
line and not line.startswith('#')]
# chec... | python | {
"resource": ""
} |
q273221 | verified_excel_file | test | def verified_excel_file(store, institute_list, temp_excel_dir):
"""Collect all verified variants in a list on institutes and save them to file
Args:
store(adapter.MongoAdapter)
institute_list(list): a list of institute ids
temp_excel_dir(os.Path): folder where the temp excel files are w... | python | {
"resource": ""
} |
q273222 | export_genes | test | def export_genes(adapter, build='37'):
"""Export all genes from the database"""
LOG.info("Exporting all genes to .bed format")
for gene_obj in adapter.all_genes(build=build):
yield gene_obj | python | {
"resource": ""
} |
q273223 | parse_clnsig | test | def parse_clnsig(acc, sig, revstat, transcripts):
"""Get the clnsig information
Args:
acc(str): The clnsig accession number, raw from vcf
sig(str): The clnsig significance score, raw from vcf
revstat(str): The clnsig revstat, raw from vcf
transcripts(iterable(dict))
Returns... | python | {
"resource": ""
} |
q273224 | parse_compounds | test | def parse_compounds(compound_info, case_id, variant_type):
"""Get a list with compounds objects for this variant.
Arguments:
compound_info(str): A Variant dictionary
case_id (str): unique family id
variant_type(str): 'research' or 'clinical'
Returns:
... | python | {
"resource": ""
} |
q273225 | genes | test | def genes(context, build, json):
"""Export all genes from a build"""
LOG.info("Running scout export genes")
adapter = context.obj['adapter']
result = adapter.all_genes(build=build)
if json:
click.echo(dumps(result))
return
gene_string = ("{0}\t{1}\t{2}\t{3}\t{4}")
c... | python | {
"resource": ""
} |
q273226 | build_individual | test | def build_individual(ind):
"""Build a Individual object
Args:
ind (dict): A dictionary with individual information
Returns:
ind_obj (dict): A Individual object
dict(
individual_id = str, # required
display_name = str,
sex = str,
... | python | {
"resource": ""
} |
q273227 | variants | test | def variants(context, case_id, institute, force, cancer, cancer_research, sv,
sv_research, snv, snv_research, str_clinical, chrom, start, end, hgnc_id,
hgnc_symbol, rank_treshold):
"""Upload variants to a case
Note that the files has to be linked with the case,
if they ... | python | {
"resource": ""
} |
q273228 | case | test | def case(institute_id, case_name):
"""Return a variant."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
if case_obj is None:
return abort(404)
return Response(json_util.dumps(case_obj), mimetype='application/json') | python | {
"resource": ""
} |
q273229 | collections | test | def collections(context):
"""Show all collections in the database"""
LOG.info("Running scout view collections")
adapter = context.obj['adapter']
for collection_name in adapter.collections():
click.echo(collection_name) | python | {
"resource": ""
} |
q273230 | institute | test | def institute(ctx, internal_id, display_name, sanger_recipients):
"""
Create a new institute and add it to the database
"""
adapter = ctx.obj['adapter']
if not internal_id:
logger.warning("A institute has to have an internal id")
ctx.abort()
if not display_name:
displa... | python | {
"resource": ""
} |
q273231 | institute | test | def institute(context, institute_id, sanger_recipient, coverage_cutoff, frequency_cutoff,
display_name, remove_sanger):
"""
Update an institute
"""
adapter = context.obj['adapter']
LOG.info("Running scout update institute")
try:
adapter.update_institute(
i... | python | {
"resource": ""
} |
q273232 | get_file_handle | test | def get_file_handle(file_path):
"""Return a opened file"""
if file_path.endswith('.gz'):
file_handle = getreader('utf-8')(gzip.open(file_path, 'r'), errors='replace')
else:
file_handle = open(file_path, 'r', encoding='utf-8')
return file_handle | python | {
"resource": ""
} |
q273233 | get_net | test | def get_net(req):
"""Get the net of any 'next' and 'prev' querystrings."""
try:
nxt, prev = map(
int, (req.GET.get('cal_next', 0), req.GET.get('cal_prev', 0))
)
net = nxt - prev
except Exception:
net = 0
return net | python | {
"resource": ""
} |
q273234 | get_next_and_prev | test | def get_next_and_prev(net):
"""Returns what the next and prev querystrings should be."""
if net == 0:
nxt = prev = 1
elif net > 0:
nxt = net + 1
prev = -(net - 1)
else:
nxt = net + 1
prev = abs(net) + 1
return nxt, prev | python | {
"resource": ""
} |
q273235 | _check_year | test | def _check_year(year, month, error, error_msg):
"""Checks that the year is within 50 years from now."""
if year not in xrange((now.year - 50), (now.year + 51)):
year = now.year
month = now.month
error = error_msg
return year, month, error | python | {
"resource": ""
} |
q273236 | check_weekday | test | def check_weekday(year, month, day, reverse=False):
"""
Make sure any event day we send back for weekday repeating
events is not a weekend.
"""
d = date(year, month, day)
while d.weekday() in (5, 6):
if reverse:
d -= timedelta(days=1)
else:
d += timedelta(... | python | {
"resource": ""
} |
q273237 | parse_case_data | test | def parse_case_data(config=None, ped=None, owner=None, vcf_snv=None,
vcf_sv=None, vcf_cancer=None, vcf_str=None, peddy_ped=None,
peddy_sex=None, peddy_check=None, delivery_report=None, multiqc=None):
"""Parse all data necessary for loading a case into scout
This can be d... | python | {
"resource": ""
} |
q273238 | add_peddy_information | test | def add_peddy_information(config_data):
"""Add information from peddy outfiles to the individuals"""
ped_info = {}
ped_check = {}
sex_check = {}
relations = []
if config_data.get('peddy_ped'):
file_handle = open(config_data['peddy_ped'], 'r')
for ind_info in parse_peddy_ped(file... | python | {
"resource": ""
} |
q273239 | parse_individual | test | def parse_individual(sample):
"""Parse individual information
Args:
sample (dict)
Returns:
{
'individual_id': str,
'father': str,
'mother': str,
'display_name': str,
'sex': str,
... | python | {
"resource": ""
} |
q273240 | parse_individuals | test | def parse_individuals(samples):
"""Parse the individual information
Reformat sample information to proper individuals
Args:
samples(list(dict))
Returns:
individuals(list(dict))
"""
individuals = []
if len(samples) == 0:
raise PedigreeError("No s... | python | {
"resource": ""
} |
q273241 | parse_case | test | def parse_case(config):
"""Parse case information from config or PED files.
Args:
config (dict): case config with detailed information
Returns:
dict: parsed case data
"""
if 'owner' not in config:
raise ConfigError("A case has to have a owner")
if 'family' not in confi... | python | {
"resource": ""
} |
q273242 | parse_ped | test | def parse_ped(ped_stream, family_type='ped'):
"""Parse out minimal family information from a PED file.
Args:
ped_stream(iterable(str))
family_type(str): Format of the pedigree information
Returns:
family_id(str), samples(list[dict])
"""
pedigree = FamilyParser(ped_stream, f... | python | {
"resource": ""
} |
q273243 | build_evaluation | test | def build_evaluation(variant_specific, variant_id, user_id, user_name,
institute_id, case_id, classification, criteria):
"""Build a evaluation object ready to be inserted to database
Args:
variant_specific(str): md5 string for the specific variant
variant_id(str): md5 strin... | python | {
"resource": ""
} |
q273244 | mt_report | test | def mt_report(context, case_id, test, outpath=None):
"""Export all mitochondrial variants for each sample of a case
and write them to an excel file
Args:
adapter(MongoAdapter)
case_id(str)
test(bool): True if the function is called for testing purposes
... | python | {
"resource": ""
} |
q273245 | is_pathogenic | test | def is_pathogenic(pvs, ps_terms, pm_terms, pp_terms):
"""Check if the criterias for Pathogenic is fullfilled
The following are descriptions of Pathogenic clasification from ACMG paper:
Pathogenic
(i) 1 Very strong (PVS1) AND
(a) ≥1 Strong (PS1–PS4) OR
(b) ≥2 Moderate (PM1–PM6) OR
... | python | {
"resource": ""
} |
q273246 | is_likely_pathogenic | test | def is_likely_pathogenic(pvs, ps_terms, pm_terms, pp_terms):
"""Check if the criterias for Likely Pathogenic is fullfilled
The following are descriptions of Likely Pathogenic clasification from ACMG paper:
Likely pathogenic
(i) 1 Very strong (PVS1) AND 1 moderate (PM1– PM6) OR
(ii) 1 Strong (P... | python | {
"resource": ""
} |
q273247 | is_likely_benign | test | def is_likely_benign(bs_terms, bp_terms):
"""Check if criterias for Likely Benign are fullfilled
The following are descriptions of Likely Benign clasification from ACMG paper:
Likely Benign
(i) 1 Strong (BS1–BS4) and 1 supporting (BP1– BP7) OR
(ii) ≥2 Supporting (BP1–BP7)
Args:
bs... | python | {
"resource": ""
} |
q273248 | get_acmg | test | def get_acmg(acmg_terms):
"""Use the algorithm described in ACMG paper to get a ACMG calssification
Args:
acmg_terms(set(str)): A collection of prediction terms
Returns:
prediction(int):
0 - Uncertain Significanse
1 - Benign
2 - Likely Benign... | python | {
"resource": ""
} |
q273249 | VariantHandler.add_gene_info | test | def add_gene_info(self, variant_obj, gene_panels=None):
"""Add extra information about genes from gene panels
Args:
variant_obj(dict): A variant from the database
gene_panels(list(dict)): List of panels from database
"""
gene_panels = gene_panels or []
#... | python | {
"resource": ""
} |
q273250 | VariantHandler.variants | test | def variants(self, case_id, query=None, variant_ids=None, category='snv',
nr_of_variants=10, skip=0, sort_key='variant_rank'):
"""Returns variants specified in question for a specific case.
If skip not equal to 0 skip the first n variants.
Arguments:
case_id(str): ... | python | {
"resource": ""
} |
q273251 | VariantHandler.sanger_variants | test | def sanger_variants(self, institute_id=None, case_id=None):
"""Return all variants with sanger information
Args:
institute_id(str)
case_id(str)
Returns:
res(pymongo.Cursor): A Cursor with all variants with sanger activity
"""
query = {'valida... | python | {
"resource": ""
} |
q273252 | VariantHandler.variant | test | def variant(self, document_id, gene_panels=None, case_id=None):
"""Returns the specified variant.
Arguments:
document_id : A md5 key that represents the variant or "variant_id"
gene_panels(List[GenePanel])
case_id (str): case id (will search with "variant... | python | {
"resource": ""
} |
q273253 | VariantHandler.gene_variants | test | def gene_variants(self, query=None,
category='snv', variant_type=['clinical'],
nr_of_variants=50, skip=0):
"""Return all variants seen in a given gene.
If skip not equal to 0 skip the first n variants.
Arguments:
query(dict): A dictionary with ... | python | {
"resource": ""
} |
q273254 | VariantHandler.verified | test | def verified(self, institute_id):
"""Return all verified variants for a given institute
Args:
institute_id(str): institute id
Returns:
res(list): a list with validated variants
"""
query = {
'verb' : 'validate',
'institute' : inst... | python | {
"resource": ""
} |
q273255 | VariantHandler.get_causatives | test | def get_causatives(self, institute_id, case_id=None):
"""Return all causative variants for an institute
Args:
institute_id(str)
case_id(str)
Yields:
str: variant document id
"""
causatives = []
if case_id:
... | python | {
"resource": ""
} |
q273256 | VariantHandler.check_causatives | test | def check_causatives(self, case_obj=None, institute_obj=None):
"""Check if there are any variants that are previously marked causative
Loop through all variants that are marked 'causative' for an
institute and check if any of the variants are present in the
current case.
... | python | {
"resource": ""
} |
q273257 | VariantHandler.other_causatives | test | def other_causatives(self, case_obj, variant_obj):
"""Find the same variant in other cases marked causative.
Args:
case_obj(dict)
variant_obj(dict)
Yields:
other_variant(dict)
"""
# variant id without "*_[variant_type]"
variant_id = v... | python | {
"resource": ""
} |
q273258 | VariantHandler.delete_variants | test | def delete_variants(self, case_id, variant_type, category=None):
"""Delete variants of one type for a case
This is used when a case is reanalyzed
Args:
case_id(str): The case id
variant_type(str): 'research' or 'clinical'
category(str): '... | python | {
"resource": ""
} |
q273259 | VariantHandler.overlapping | test | def overlapping(self, variant_obj):
"""Return overlapping variants.
Look at the genes that a variant overlaps to.
Then return all variants that overlap these genes.
If variant_obj is sv it will return the overlapping snvs and oposite
There is a problem when SVs are huge since t... | python | {
"resource": ""
} |
q273260 | VariantHandler.evaluated_variants | test | def evaluated_variants(self, case_id):
"""Returns variants that has been evaluated
Return all variants, snvs/indels and svs from case case_id
which have a entry for 'acmg_classification', 'manual_rank', 'dismiss_variant'
or if they are commented.
Args:
case_id(str)
... | python | {
"resource": ""
} |
q273261 | VariantHandler.get_region_vcf | test | def get_region_vcf(self, case_obj, chrom=None, start=None, end=None,
gene_obj=None, variant_type='clinical', category='snv',
rank_threshold=None):
"""Produce a reduced vcf with variants from the specified coordinates
This is used for the alignment viewer.... | python | {
"resource": ""
} |
q273262 | VariantHandler.sample_variants | test | def sample_variants(self, variants, sample_name, category = 'snv'):
"""Given a list of variants get variant objects found in a specific patient
Args:
variants(list): a list of variant ids
sample_name(str): a sample display name
category(str): 'snv', 'sv' ..
... | python | {
"resource": ""
} |
q273263 | get_connection | test | def get_connection(host='localhost', port=27017, username=None, password=None,
uri=None, mongodb=None, authdb=None, timeout=20, *args, **kwargs):
"""Get a client to the mongo database
host(str): Host of database
port(int): Port of database
username(str)
password(s... | python | {
"resource": ""
} |
q273264 | get_objects_from_form | test | def get_objects_from_form(variant_ids, form_fields, object_type):
"""Extract the objects to be saved in the clinvar database collection.
object_type param specifies if these objects are variant or casedata objects
Args:
variant_ids(list): list of database variant ids
form_fields(dict)... | python | {
"resource": ""
} |
q273265 | clinvar_submission_header | test | def clinvar_submission_header(submission_objs, csv_type):
"""Determine which fields to include in csv header by checking a list of submission objects
Args:
submission_objs(list): a list of objects (variants or casedata) to include in a csv file
csv_type(str) : 'variant_data' or 'cas... | python | {
"resource": ""
} |
q273266 | clinvar_submission_lines | test | def clinvar_submission_lines(submission_objs, submission_header):
"""Create the lines to include in a Clinvar submission csv file from a list of submission objects and a custom document header
Args:
submission_objs(list): a list of objects (variants or casedata) to include in a csv file
... | python | {
"resource": ""
} |
q273267 | load_transcripts | test | def load_transcripts(adapter, transcripts_lines=None, build='37', ensembl_genes=None):
"""Load all the transcripts
Transcript information is from ensembl.
Args:
adapter(MongoAdapter)
transcripts_lines(iterable): iterable with ensembl transcript lines
build(str)
ensembl_gene... | python | {
"resource": ""
} |
q273268 | panel | test | def panel(context, path, date, display_name, version, panel_type, panel_id, institute, omim, api_key, panel_app):
"""Add a gene panel to the database."""
adapter = context.obj['adapter']
institute = institute or 'cust000'
if omim:
api_key = api_key or context.obj.get('omim_api_key')
if... | python | {
"resource": ""
} |
q273269 | build_exon | test | def build_exon(exon_info, build='37'):
"""Build a Exon object object
Args:
exon_info(dict): Exon information
Returns:
exon_obj(Exon)
"exon_id": str, # str(chrom-start-end)
"chrom": str,
"start": int,
"end": int,
"trans... | python | {
"resource": ""
} |
q273270 | panel | test | def panel(context, panel_id, version):
"""Delete a version of a gene panel or all versions of a gene panel"""
LOG.info("Running scout delete panel")
adapter = context.obj['adapter']
panel_objs = adapter.gene_panels(panel_id=panel_id, version=version)
if panel_objs.count() == 0:
LOG.info("No... | python | {
"resource": ""
} |
q273271 | index | test | def index(context):
"""Delete all indexes in the database"""
LOG.info("Running scout delete index")
adapter = context.obj['adapter']
for collection in adapter.db.collection_names():
adapter.db[collection].drop_indexes()
LOG.info("All indexes deleted") | python | {
"resource": ""
} |
q273272 | user | test | def user(context, mail):
"""Delete a user from the database"""
LOG.info("Running scout delete user")
adapter = context.obj['adapter']
user_obj = adapter.user(mail)
if not user_obj:
LOG.warning("User {0} could not be found in database".format(mail))
else:
adapter.delete_user(mail) | python | {
"resource": ""
} |
q273273 | genes | test | def genes(context, build):
"""Delete all genes in the database"""
LOG.info("Running scout delete genes")
adapter = context.obj['adapter']
if build:
LOG.info("Dropping genes collection for build: %s", build)
else:
LOG.info("Dropping genes collection")
adapter.drop_genes() | python | {
"resource": ""
} |
q273274 | exons | test | def exons(context, build):
"""Delete all exons in the database"""
LOG.info("Running scout delete exons")
adapter = context.obj['adapter']
adapter.drop_exons(build) | python | {
"resource": ""
} |
q273275 | case | test | def case(context, institute, case_id, display_name):
"""Delete a case and it's variants from the database"""
adapter = context.obj['adapter']
if not (case_id or display_name):
click.echo("Please specify what case to delete")
context.abort()
if display_name:
if not institute:
... | python | {
"resource": ""
} |
q273276 | individuals | test | def individuals(context, institute, causatives, case_id):
"""Show all individuals from all cases in the database"""
LOG.info("Running scout view individuals")
adapter = context.obj['adapter']
individuals = []
if case_id:
case = adapter.case(case_id=case_id)
if case:
case... | python | {
"resource": ""
} |
q273277 | parse_matches | test | def parse_matches(patient_id, match_objs):
"""Parse a list of matchmaker matches objects and returns
a readable list of matches to display in matchmaker matches view.
Args:
patient_id(str): id of a mme patient
match_objs(list): list of match objs returned by MME server for the patient
... | python | {
"resource": ""
} |
q273278 | cases | test | def cases(context, institute, display_name, case_id, nr_variants, variants_treshold):
"""Display cases from the database"""
LOG.info("Running scout view institutes")
adapter = context.obj['adapter']
models = []
if case_id:
case_obj = adapter.case(case_id=case_id)
if case_obj:
... | python | {
"resource": ""
} |
q273279 | load_user | test | def load_user(user_email):
"""Returns the currently active user as an object."""
user_obj = store.user(user_email)
user_inst = LoginUser(user_obj) if user_obj else None
return user_inst | python | {
"resource": ""
} |
q273280 | login | test | def login():
"""Login a user if they have access."""
# store potential next param URL in the session
if 'next' in request.args:
session['next_url'] = request.args['next']
if current_app.config.get('GOOGLE'):
callback_url = url_for('.authorized', _external=True)
return google.aut... | python | {
"resource": ""
} |
q273281 | build_institute | test | def build_institute(internal_id, display_name, sanger_recipients=None,
coverage_cutoff=None, frequency_cutoff=None):
"""Build a institute object
Args:
internal_id(str)
display_name(str)
sanger_recipients(list(str)): List with email addresses
Returns:
ins... | python | {
"resource": ""
} |
q273282 | EventHandler.delete_event | test | def delete_event(self, event_id):
"""Delete a event
Arguments:
event_id (str): The database key for the event
"""
LOG.info("Deleting event{0}".format(event_id))
if not isinstance(event_id, ObjectId):
event_id = ObjectId(event_id)
self.even... | python | {
"resource": ""
} |
q273283 | EventHandler.create_event | test | def create_event(self, institute, case, user, link, category, verb,
subject, level='specific', variant=None, content=None,
panel=None):
"""Create a Event with the parameters given.
Arguments:
institute (dict): A institute
case (dict): A ... | python | {
"resource": ""
} |
q273284 | EventHandler.events | test | def events(self, institute, case=None, variant_id=None, level=None,
comments=False, panel=None):
"""Fetch events from the database.
Args:
institute (dict): A institute
case (dict): A case
variant_id (str, optional): global variant id
leve... | python | {
"resource": ""
} |
q273285 | EventHandler.user_events | test | def user_events(self, user_obj=None):
"""Fetch all events by a specific user."""
query = dict(user_id=user_obj['_id']) if user_obj else dict()
return self.event_collection.find(query) | python | {
"resource": ""
} |
q273286 | EventHandler.add_phenotype | test | def add_phenotype(self, institute, case, user, link, hpo_term=None,
omim_term=None, is_group=False):
"""Add a new phenotype term to a case
Create a phenotype term and event with the given information
Args:
institute (Institute): A Institute object
... | python | {
"resource": ""
} |
q273287 | EventHandler.remove_phenotype | test | def remove_phenotype(self, institute, case, user, link, phenotype_id,
is_group=False):
"""Remove an existing phenotype from a case
Args:
institute (dict): A Institute object
case (dict): Case object
user (dict): A User object
link... | python | {
"resource": ""
} |
q273288 | EventHandler.comment | test | def comment(self, institute, case, user, link, variant=None,
content="", comment_level="specific"):
"""Add a comment to a variant or a case.
This function will create an Event to log that a user have commented on
a variant. If a variant id is given it will be a variant comment.
... | python | {
"resource": ""
} |
q273289 | parse_genotypes | test | def parse_genotypes(variant, individuals, individual_positions):
"""Parse the genotype calls for a variant
Args:
variant(cyvcf2.Variant)
individuals: List[dict]
individual_positions(dict)
Returns:
genotypes(list(dict)): A list of genotypes
"""
... | python | {
"resource": ""
} |
q273290 | check_coordinates | test | def check_coordinates(chromosome, pos, coordinates):
"""Check if the variant is in the interval given by the coordinates
Args:
chromosome(str): Variant chromosome
pos(int): Variant position
coordinates(dict): Dictionary with the region of interest
"""
chrom_match... | python | {
"resource": ""
} |
q273291 | hpo_terms | test | def hpo_terms():
"""Render search box and view for HPO phenotype terms"""
if request.method == 'GET':
data = controllers.hpo_terms(store= store, limit=100)
return data
else: # POST. user is searching for a specific term or phenotype
search_term = request.form.get('hpo_term')
... | python | {
"resource": ""
} |
q273292 | transcripts | test | def transcripts(context, build):
"""Export all transcripts to .bed like format"""
LOG.info("Running scout export transcripts")
adapter = context.obj['adapter']
header = ["#Chrom\tStart\tEnd\tTranscript\tRefSeq\tHgncID"]
for line in header:
click.echo(line)
transcript_string = ("{0... | python | {
"resource": ""
} |
q273293 | exons | test | def exons(context, build):
"""Load exons into the scout database"""
adapter = context.obj['adapter']
start = datetime.now()
# Test if there are any exons loaded
nr_exons = adapter.exons(build=build).count()
if nr_exons:
LOG.warning("Dropping all exons ")
adapter.dr... | python | {
"resource": ""
} |
q273294 | region | test | def region(context, hgnc_id, case_id, chromosome, start, end):
"""Load all variants in a region to a existing case"""
adapter = context.obj['adapter']
load_region(
adapter=adapter, case_id=case_id, hgnc_id=hgnc_id, chrom=chromosome, start=start, end=end
) | python | {
"resource": ""
} |
q273295 | EventManager.all_month_events | test | def all_month_events(self, year, month, category=None, tag=None,
loc=False, cncl=False):
"""
Returns all events that have an occurrence within the given
month & year.
"""
kwargs = self._get_kwargs(category, tag)
ym_first, ym_last = self.get_first_... | python | {
"resource": ""
} |
q273296 | EventManager.live | test | def live(self, now):
"""
Returns a queryset of events that will occur again after 'now'.
Used to help generate a list of upcoming events.
"""
return self.model.objects.filter(
Q(end_repeat=None) | Q(end_repeat__gte=now) |
Q(start_date__gte=now) | Q(end_dat... | python | {
"resource": ""
} |
q273297 | parse_reqs | test | def parse_reqs(req_path='./requirements.txt'):
"""Recursively parse requirements from nested pip files."""
install_requires = []
with io.open(os.path.join(here, 'requirements.txt'), encoding='utf-8') as handle:
# remove comments and empty lines
lines = (line.strip() for line in handle
... | python | {
"resource": ""
} |
q273298 | existing_gene | test | def existing_gene(store, panel_obj, hgnc_id):
"""Check if gene is already added to a panel."""
existing_genes = {gene['hgnc_id']: gene for gene in panel_obj['genes']}
return existing_genes.get(hgnc_id) | python | {
"resource": ""
} |
q273299 | update_panel | test | def update_panel(store, panel_name, csv_lines, option):
"""Update an existing gene panel with genes.
Args:
store(scout.adapter.MongoAdapter)
panel_name(str)
csv_lines(iterable(str)): Stream with genes
option(str): 'add' or 'replace'
Returns:
panel_obj(dict)
"""
... | python | {
"resource": ""
} |
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