partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
test | archive_info | Get information about a case from archive. | scripts/transfer-archive.py | def archive_info(database: Database, archive_case: dict) -> dict:
"""Get information about a case from archive."""
data = {
'collaborators': archive_case['collaborators'],
'synopsis': archive_case.get('synopsis'),
'assignees': [],
'suspects': [],
'causatives': [],
... | def archive_info(database: Database, archive_case: dict) -> dict:
"""Get information about a case from archive."""
data = {
'collaborators': archive_case['collaborators'],
'synopsis': archive_case.get('synopsis'),
'assignees': [],
'suspects': [],
'causatives': [],
... | [
"Get",
"information",
"about",
"a",
"case",
"from",
"archive",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scripts/transfer-archive.py#L26-L59 | [
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test | migrate_case | Migrate case information from archive. | scripts/transfer-archive.py | def migrate_case(adapter: MongoAdapter, scout_case: dict, archive_data: dict):
"""Migrate case information from archive."""
# update collaborators
collaborators = list(set(scout_case['collaborators'] + archive_data['collaborators']))
if collaborators != scout_case['collaborators']:
LOG.info(f"se... | def migrate_case(adapter: MongoAdapter, scout_case: dict, archive_data: dict):
"""Migrate case information from archive."""
# update collaborators
collaborators = list(set(scout_case['collaborators'] + archive_data['collaborators']))
if collaborators != scout_case['collaborators']:
LOG.info(f"se... | [
"Migrate",
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"information",
"from",
"archive",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scripts/transfer-archive.py#L62-L116 | [
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"ar... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | migrate | Update all information that was manually annotated from a old instance. | scripts/transfer-archive.py | def migrate(uri: str, archive_uri: str, case_id: str, dry: bool, force: bool):
"""Update all information that was manually annotated from a old instance."""
scout_client = MongoClient(uri)
scout_database = scout_client[uri.rsplit('/', 1)[-1]]
scout_adapter = MongoAdapter(database=scout_database)
sco... | def migrate(uri: str, archive_uri: str, case_id: str, dry: bool, force: bool):
"""Update all information that was manually annotated from a old instance."""
scout_client = MongoClient(uri)
scout_database = scout_client[uri.rsplit('/', 1)[-1]]
scout_adapter = MongoAdapter(database=scout_database)
sco... | [
"Update",
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"information",
"that",
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"from",
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"old",
"instance",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scripts/transfer-archive.py#L125-L148 | [
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test | research | Upload research variants to cases
If a case is specified, all variants found for that case will be
uploaded.
If no cases are specified then all cases that have 'research_requested'
will have there research variants uploaded | scout/commands/load/research.py | def research(context, case_id, institute, force):
"""Upload research variants to cases
If a case is specified, all variants found for that case will be
uploaded.
If no cases are specified then all cases that have 'research_requested'
will have there research variants uploaded
"... | def research(context, case_id, institute, force):
"""Upload research variants to cases
If a case is specified, all variants found for that case will be
uploaded.
If no cases are specified then all cases that have 'research_requested'
will have there research variants uploaded
"... | [
"Upload",
"research",
"variants",
"to",
"cases"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/load/research.py#L14-L101 | [
"def",
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | load_hgnc | Load Genes and transcripts into the database
If no resources are provided the correct ones will be fetched.
Args:
adapter(scout.adapter.MongoAdapter)
genes(dict): If genes are already parsed
ensembl_lines(iterable(str)): Lines formated with ensembl gene information
... | scout/load/hgnc_gene.py | def load_hgnc(adapter, genes=None, ensembl_lines=None, hgnc_lines=None, exac_lines=None, mim2gene_lines=None,
genemap_lines=None, hpo_lines=None, transcripts_lines=None, build='37', omim_api_key=''):
"""Load Genes and transcripts into the database
If no resources are provided the co... | def load_hgnc(adapter, genes=None, ensembl_lines=None, hgnc_lines=None, exac_lines=None, mim2gene_lines=None,
genemap_lines=None, hpo_lines=None, transcripts_lines=None, build='37', omim_api_key=''):
"""Load Genes and transcripts into the database
If no resources are provided the co... | [
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"... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/load/hgnc_gene.py#L19-L59 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | load_hgnc_genes | Load genes into the database
link_genes will collect information from all the different sources and
merge it into a dictionary with hgnc_id as key and gene information as values.
Args:
adapter(scout.adapter.MongoAdapter)
genes(dict): If genes are already parsed
ensembl_lin... | scout/load/hgnc_gene.py | def load_hgnc_genes(adapter, genes = None, ensembl_lines=None, hgnc_lines=None, exac_lines=None, mim2gene_lines=None,
genemap_lines=None, hpo_lines=None, build='37', omim_api_key=''):
"""Load genes into the database
link_genes will collect information from all the different sources ... | def load_hgnc_genes(adapter, genes = None, ensembl_lines=None, hgnc_lines=None, exac_lines=None, mim2gene_lines=None,
genemap_lines=None, hpo_lines=None, build='37', omim_api_key=''):
"""Load genes into the database
link_genes will collect information from all the different sources ... | [
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"with",
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"as",
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"valu... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/load/hgnc_gene.py#L61-L130 | [
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",",
"hpo_lines",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | hpo | Show all hpo terms in the database | scout/commands/view/hpo.py | def hpo(context, term, description):
"""Show all hpo terms in the database"""
LOG.info("Running scout view hpo")
adapter = context.obj['adapter']
if term:
term = term.upper()
if not term.startswith('HP:'):
while len(term) < 7:
term = '0' + term
ter... | def hpo(context, term, description):
"""Show all hpo terms in the database"""
LOG.info("Running scout view hpo")
adapter = context.obj['adapter']
if term:
term = term.upper()
if not term.startswith('HP:'):
while len(term) < 7:
term = '0' + term
ter... | [
"Show",
"all",
"hpo",
"terms",
"in",
"the",
"database"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/view/hpo.py#L14-L45 | [
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"("... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | build_gene | Build a gene object
Has to build the transcripts for the genes to
Args:
gene(dict): Parsed information from the VCF
hgncid_to_gene(dict): A map from hgnc_id -> hgnc_gene objects
Returns:
gene_obj(dict)
gene = dict(
# The hgnc gene id
hgnc... | scout/build/variant/gene.py | def build_gene(gene, hgncid_to_gene=None):
"""Build a gene object
Has to build the transcripts for the genes to
Args:
gene(dict): Parsed information from the VCF
hgncid_to_gene(dict): A map from hgnc_id -> hgnc_gene objects
Returns:
gene_obj(dict)
ge... | def build_gene(gene, hgncid_to_gene=None):
"""Build a gene object
Has to build the transcripts for the genes to
Args:
gene(dict): Parsed information from the VCF
hgncid_to_gene(dict): A map from hgnc_id -> hgnc_gene objects
Returns:
gene_obj(dict)
ge... | [
"Build",
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"fr... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/build/variant/gene.py#L9-L99 | [
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"=",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | create_app | Flask app factory function. | scout/server/app.py | def create_app(config_file=None, config=None):
"""Flask app factory function."""
app = Flask(__name__)
app.config.from_pyfile('config.py')
app.jinja_env.add_extension('jinja2.ext.do')
if config:
app.config.update(config)
if config_file:
app.config.from_pyfile(config_file)
# ... | def create_app(config_file=None, config=None):
"""Flask app factory function."""
app = Flask(__name__)
app.config.from_pyfile('config.py')
app.jinja_env.add_extension('jinja2.ext.do')
if config:
app.config.update(config)
if config_file:
app.config.from_pyfile(config_file)
# ... | [
"Flask",
"app",
"factory",
"function",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/app.py#L35-L76 | [
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test | configure_extensions | Configure Flask extensions. | scout/server/app.py | def configure_extensions(app):
"""Configure Flask extensions."""
extensions.toolbar.init_app(app)
extensions.bootstrap.init_app(app)
extensions.mongo.init_app(app)
extensions.store.init_app(app)
extensions.login_manager.init_app(app)
extensions.oauth.init_app(app)
extensions.mail.init_ap... | def configure_extensions(app):
"""Configure Flask extensions."""
extensions.toolbar.init_app(app)
extensions.bootstrap.init_app(app)
extensions.mongo.init_app(app)
extensions.store.init_app(app)
extensions.login_manager.init_app(app)
extensions.oauth.init_app(app)
extensions.mail.init_ap... | [
"Configure",
"Flask",
"extensions",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/app.py#L79-L95 | [
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test | register_blueprints | Register Flask blueprints. | scout/server/app.py | def register_blueprints(app):
"""Register Flask blueprints."""
app.register_blueprint(public.public_bp)
app.register_blueprint(genes.genes_bp)
app.register_blueprint(cases.cases_bp)
app.register_blueprint(login.login_bp)
app.register_blueprint(variants.variants_bp)
app.register_blueprint(pan... | def register_blueprints(app):
"""Register Flask blueprints."""
app.register_blueprint(public.public_bp)
app.register_blueprint(genes.genes_bp)
app.register_blueprint(cases.cases_bp)
app.register_blueprint(login.login_bp)
app.register_blueprint(variants.variants_bp)
app.register_blueprint(pan... | [
"Register",
"Flask",
"blueprints",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/app.py#L98-L110 | [
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test | configure_email_logging | Setup logging of error/exceptions to email. | scout/server/app.py | def configure_email_logging(app):
"""Setup logging of error/exceptions to email."""
import logging
from scout.log import TlsSMTPHandler
mail_handler = TlsSMTPHandler(
mailhost=app.config['MAIL_SERVER'],
fromaddr=app.config['MAIL_USERNAME'],
toaddrs=app.config['ADMINS'],
... | def configure_email_logging(app):
"""Setup logging of error/exceptions to email."""
import logging
from scout.log import TlsSMTPHandler
mail_handler = TlsSMTPHandler(
mailhost=app.config['MAIL_SERVER'],
fromaddr=app.config['MAIL_USERNAME'],
toaddrs=app.config['ADMINS'],
... | [
"Setup",
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"/",
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"email",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/app.py#L146-L163 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | configure_coverage | Setup coverage related extensions. | scout/server/app.py | def configure_coverage(app):
"""Setup coverage related extensions."""
# setup chanjo report
app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = True if app.debug else False
if chanjo_api:
chanjo_api.init_app(app)
configure_template_filters(app)
# register chanjo report blueprint
... | def configure_coverage(app):
"""Setup coverage related extensions."""
# setup chanjo report
app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = True if app.debug else False
if chanjo_api:
chanjo_api.init_app(app)
configure_template_filters(app)
# register chanjo report blueprint
... | [
"Setup",
"coverage",
"related",
"extensions",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/app.py#L166-L197 | [
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test | aliases | Show all alias symbols and how they map to ids | scout/commands/view/aliases.py | def aliases(context, build, symbol):
"""Show all alias symbols and how they map to ids"""
LOG.info("Running scout view aliases")
adapter = context.obj['adapter']
if symbol:
alias_genes = {}
res = adapter.gene_by_alias(symbol, build=build)
for gene_obj in res:
hgn... | def aliases(context, build, symbol):
"""Show all alias symbols and how they map to ids"""
LOG.info("Running scout view aliases")
adapter = context.obj['adapter']
if symbol:
alias_genes = {}
res = adapter.gene_by_alias(symbol, build=build)
for gene_obj in res:
hgn... | [
"Show",
"all",
"alias",
"symbols",
"and",
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"map",
"to",
"ids"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/view/aliases.py#L11-L56 | [
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test | build_gene | Build a panel_gene object
Args:
gene_info(dict)
Returns:
gene_obj(dict)
panel_gene = dict(
hgnc_id = int, # required
symbol = str,
disease_associated_transcripts = list, # list of strings that represent refseq transcripts
r... | scout/build/panel.py | def build_gene(gene_info, adapter):
"""Build a panel_gene object
Args:
gene_info(dict)
Returns:
gene_obj(dict)
panel_gene = dict(
hgnc_id = int, # required
symbol = str,
disease_associated_transcripts = list, # list of strings that... | def build_gene(gene_info, adapter):
"""Build a panel_gene object
Args:
gene_info(dict)
Returns:
gene_obj(dict)
panel_gene = dict(
hgnc_id = int, # required
symbol = str,
disease_associated_transcripts = list, # list of strings that... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/build/panel.py#L10-L87 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | build_panel | Build a gene_panel object
Args:
panel_info(dict): A dictionary with panel information
adapter (scout.adapter.MongoAdapter)
Returns:
panel_obj(dict)
gene_panel = dict(
panel_id = str, # required
institute = str, # institute_id, required
v... | scout/build/panel.py | def build_panel(panel_info, adapter):
"""Build a gene_panel object
Args:
panel_info(dict): A dictionary with panel information
adapter (scout.adapter.MongoAdapter)
Returns:
panel_obj(dict)
gene_panel = dict(
panel_id = str, # required
instit... | def build_panel(panel_info, adapter):
"""Build a gene_panel object
Args:
panel_info(dict): A dictionary with panel information
adapter (scout.adapter.MongoAdapter)
Returns:
panel_obj(dict)
gene_panel = dict(
panel_id = str, # required
instit... | [
"Build",
"a",
"gene_panel",
"object"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/build/panel.py#L90-L154 | [
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test | verified | Export variants which have been verified for an institute
and write them to an excel file.
Args:
collaborator(str): institute id
test(bool): True if the function is called for testing purposes
outpath(str): path to output file
Returns:
written_files(int): number of writ... | scout/commands/export/variant.py | def verified(context, collaborator, test, outpath=None):
"""Export variants which have been verified for an institute
and write them to an excel file.
Args:
collaborator(str): institute id
test(bool): True if the function is called for testing purposes
outpath(str): path to outp... | def verified(context, collaborator, test, outpath=None):
"""Export variants which have been verified for an institute
and write them to an excel file.
Args:
collaborator(str): institute id
test(bool): True if the function is called for testing purposes
outpath(str): path to outp... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/export/variant.py#L29-L87 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | variants | Export causatives for a collaborator in .vcf format | scout/commands/export/variant.py | def variants(context, collaborator, document_id, case_id, json):
"""Export causatives for a collaborator in .vcf format"""
LOG.info("Running scout export variants")
adapter = context.obj['adapter']
collaborator = collaborator or 'cust000'
variants = export_variants(
adapter,
collabo... | def variants(context, collaborator, document_id, case_id, json):
"""Export causatives for a collaborator in .vcf format"""
LOG.info("Running scout export variants")
adapter = context.obj['adapter']
collaborator = collaborator or 'cust000'
variants = export_variants(
adapter,
collabo... | [
"Export",
"causatives",
"for",
"a",
"collaborator",
"in",
".",
"vcf",
"format"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/export/variant.py#L102-L135 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_vcf_entry | Get vcf entry from variant object
Args:
variant_obj(dict)
Returns:
variant_string(str): string representing variant in vcf format | scout/commands/export/variant.py | def get_vcf_entry(variant_obj, case_id=None):
"""
Get vcf entry from variant object
Args:
variant_obj(dict)
Returns:
variant_string(str): string representing variant in vcf format
"""
if variant_obj['category'] == 'snv':
var_type = 'TYPE'
else:
... | def get_vcf_entry(variant_obj, case_id=None):
"""
Get vcf entry from variant object
Args:
variant_obj(dict)
Returns:
variant_string(str): string representing variant in vcf format
"""
if variant_obj['category'] == 'snv':
var_type = 'TYPE'
else:
... | [
"Get",
"vcf",
"entry",
"from",
"variant",
"object"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/export/variant.py#L138-L175 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | serve | Start the web server. | scout/commands/serve.py | def serve(context, config, host, port, debug, livereload):
"""Start the web server."""
pymongo_config = dict(
MONGO_HOST=context.obj['host'],
MONGO_PORT=context.obj['port'],
MONGO_DBNAME=context.obj['mongodb'],
MONGO_USERNAME=context.obj['username'],
MONGO_PASSWORD=contex... | def serve(context, config, host, port, debug, livereload):
"""Start the web server."""
pymongo_config = dict(
MONGO_HOST=context.obj['host'],
MONGO_PORT=context.obj['port'],
MONGO_DBNAME=context.obj['mongodb'],
MONGO_USERNAME=context.obj['username'],
MONGO_PASSWORD=contex... | [
"Start",
"the",
"web",
"server",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/serve.py#L22-L53 | [
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"."... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | generate_md5_key | Generate an md5-key from a list of arguments.
Args:
list_of_arguments: A list of strings
Returns:
A md5-key object generated from the list of strings. | scout/utils/md5.py | def generate_md5_key(list_of_arguments):
"""
Generate an md5-key from a list of arguments.
Args:
list_of_arguments: A list of strings
Returns:
A md5-key object generated from the list of strings.
"""
for arg in list_of_arguments:
if not isinstance(arg, string_types):
... | def generate_md5_key(list_of_arguments):
"""
Generate an md5-key from a list of arguments.
Args:
list_of_arguments: A list of strings
Returns:
A md5-key object generated from the list of strings.
"""
for arg in list_of_arguments:
if not isinstance(arg, string_types):
... | [
"Generate",
"an",
"md5",
"-",
"key",
"from",
"a",
"list",
"of",
"arguments",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/md5.py#L6-L23 | [
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"\"Argument: {0} is a {1}... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | MongoAdapter.init_app | Setup via Flask. | scout/adapter/mongo/base.py | def init_app(self, app):
"""Setup via Flask."""
host = app.config.get('MONGO_HOST', 'localhost')
port = app.config.get('MONGO_PORT', 27017)
dbname = app.config['MONGO_DBNAME']
log.info("connecting to database: %s:%s/%s", host, port, dbname)
self.setup(app.config['MONGO_DA... | def init_app(self, app):
"""Setup via Flask."""
host = app.config.get('MONGO_HOST', 'localhost')
port = app.config.get('MONGO_PORT', 27017)
dbname = app.config['MONGO_DBNAME']
log.info("connecting to database: %s:%s/%s", host, port, dbname)
self.setup(app.config['MONGO_DA... | [
"Setup",
"via",
"Flask",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/base.py#L60-L66 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | MongoAdapter.setup | Setup connection to database. | scout/adapter/mongo/base.py | def setup(self, database):
"""Setup connection to database."""
self.db = database
self.hgnc_collection = database.hgnc_gene
self.user_collection = database.user
self.whitelist_collection = database.whitelist
self.institute_collection = database.institute
self.even... | def setup(self, database):
"""Setup connection to database."""
self.db = database
self.hgnc_collection = database.hgnc_gene
self.user_collection = database.user
self.whitelist_collection = database.whitelist
self.institute_collection = database.institute
self.even... | [
"Setup",
"connection",
"to",
"database",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/base.py#L68-L85 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | index | Create indexes for the database | scout/commands/index_command.py | def index(context, update):
"""Create indexes for the database"""
LOG.info("Running scout index")
adapter = context.obj['adapter']
if update:
adapter.update_indexes()
else:
adapter.load_indexes() | def index(context, update):
"""Create indexes for the database"""
LOG.info("Running scout index")
adapter = context.obj['adapter']
if update:
adapter.update_indexes()
else:
adapter.load_indexes() | [
"Create",
"indexes",
"for",
"the",
"database"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/index_command.py#L19-L27 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | database | Setup a scout database. | scout/commands/setup/setup_scout.py | def database(context, institute_name, user_name, user_mail, api_key):
"""Setup a scout database."""
LOG.info("Running scout setup database")
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key with --ap... | def database(context, institute_name, user_name, user_mail, api_key):
"""Setup a scout database."""
LOG.info("Running scout setup database")
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key with --ap... | [
"Setup",
"a",
"scout",
"database",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/setup/setup_scout.py#L46-L70 | [
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".... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | demo | Setup a scout demo instance. This instance will be populated with a
case, a gene panel and some variants. | scout/commands/setup/setup_scout.py | def demo(context):
"""Setup a scout demo instance. This instance will be populated with a
case, a gene panel and some variants.
"""
LOG.info("Running scout setup demo")
institute_name = context.obj['institute_name']
user_name = context.obj['user_name']
user_mail = context.obj['user_mail']... | def demo(context):
"""Setup a scout demo instance. This instance will be populated with a
case, a gene panel and some variants.
"""
LOG.info("Running scout setup demo")
institute_name = context.obj['institute_name']
user_name = context.obj['user_name']
user_mail = context.obj['user_mail']... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | setup | Setup scout instances. | scout/commands/setup/setup_scout.py | def setup(context, institute, user_mail, user_name):
"""
Setup scout instances.
"""
context.obj['institute_name'] = institute
context.obj['user_name'] = user_name
context.obj['user_mail'] = user_mail
if context.invoked_subcommand == 'demo':
# Update context.obj settings here
... | def setup(context, institute, user_mail, user_name):
"""
Setup scout instances.
"""
context.obj['institute_name'] = institute
context.obj['user_name'] = user_name
context.obj['user_mail'] = user_mail
if context.invoked_subcommand == 'demo':
# Update context.obj settings here
... | [
"Setup",
"scout",
"instances",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/setup/setup_scout.py#L118-L159 | [
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test | institutes | Show all institutes in the database | scout/commands/view/institutes.py | def institutes(context, institute_id, json):
"""Show all institutes in the database"""
LOG.info("Running scout view institutes")
adapter = context.obj['adapter']
if institute_id:
institute_objs = []
institute_obj = adapter.institute(institute_id)
if not institute_obj:
... | def institutes(context, institute_id, json):
"""Show all institutes in the database"""
LOG.info("Running scout view institutes")
adapter = context.obj['adapter']
if institute_id:
institute_objs = []
institute_obj = adapter.institute(institute_id)
if not institute_obj:
... | [
"Show",
"all",
"institutes",
"in",
"the",
"database"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/view/institutes.py#L16-L51 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_genetic_models | Parse the genetic models entry of a vcf
Args:
models_info(str): The raw vcf information
case_id(str)
Returns:
genetic_models(list) | scout/parse/variant/models.py | def parse_genetic_models(models_info, case_id):
"""Parse the genetic models entry of a vcf
Args:
models_info(str): The raw vcf information
case_id(str)
Returns:
genetic_models(list)
"""
genetic_models = []
if models_info:
for family_info in models_info.split(',... | def parse_genetic_models(models_info, case_id):
"""Parse the genetic models entry of a vcf
Args:
models_info(str): The raw vcf information
case_id(str)
Returns:
genetic_models(list)
"""
genetic_models = []
if models_info:
for family_info in models_info.split(',... | [
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"models",
"entry",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/models.py#L2-L20 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | panels | Show all gene panels in the database | scout/commands/view/panels.py | def panels(context, institute):
"""Show all gene panels in the database"""
LOG.info("Running scout view panels")
adapter = context.obj['adapter']
panel_objs = adapter.gene_panels(institute_id=institute)
if panel_objs.count() == 0:
LOG.info("No panels found")
context.abort()
clic... | def panels(context, institute):
"""Show all gene panels in the database"""
LOG.info("Running scout view panels")
adapter = context.obj['adapter']
panel_objs = adapter.gene_panels(institute_id=institute)
if panel_objs.count() == 0:
LOG.info("No panels found")
context.abort()
clic... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/view/panels.py#L12-L29 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | InstituteHandler.add_institute | Add a institute to the database
Args:
institute_obj(Institute) | scout/adapter/mongo/institute.py | def add_institute(self, institute_obj):
"""Add a institute to the database
Args:
institute_obj(Institute)
"""
internal_id = institute_obj['internal_id']
display_name = institute_obj['internal_id']
# Check if institute already exists
if self.i... | def add_institute(self, institute_obj):
"""Add a institute to the database
Args:
institute_obj(Institute)
"""
internal_id = institute_obj['internal_id']
display_name = institute_obj['internal_id']
# Check if institute already exists
if self.i... | [
"Add",
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"institute",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/institute.py#L16-L36 | [
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"institute",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | InstituteHandler.update_institute | Update the information for an institute
Args:
internal_id(str): The internal institute id
sanger_recipient(str): Email adress to add for sanger order
coverage_cutoff(int): Update coverage cutoff
frequency_cutoff(float): New frequency cutoff
display_na... | scout/adapter/mongo/institute.py | def update_institute(self, internal_id, sanger_recipient=None, coverage_cutoff=None,
frequency_cutoff=None, display_name=None, remove_sanger=None,
phenotype_groups=None, group_abbreviations=None, add_groups=None):
"""Update the information for an institute
... | def update_institute(self, internal_id, sanger_recipient=None, coverage_cutoff=None,
frequency_cutoff=None, display_name=None, remove_sanger=None,
phenotype_groups=None, group_abbreviations=None, add_groups=None):
"""Update the information for an institute
... | [
"Update",
"the",
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"institute"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/institute.py#L38-L129 | [
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"=",
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test | InstituteHandler.institute | Featch a single institute from the backend
Args:
institute_id(str)
Returns:
Institute object | scout/adapter/mongo/institute.py | def institute(self, institute_id):
"""Featch a single institute from the backend
Args:
institute_id(str)
Returns:
Institute object
"""
LOG.debug("Fetch institute {}".format(institute_id))
institute_obj = self.institute_collection.... | def institute(self, institute_id):
"""Featch a single institute from the backend
Args:
institute_id(str)
Returns:
Institute object
"""
LOG.debug("Fetch institute {}".format(institute_id))
institute_obj = self.institute_collection.... | [
"Featch",
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"single",
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"from",
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"backend"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/institute.py#L131-L147 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | InstituteHandler.institutes | Fetch all institutes.
Args:
institute_ids(list(str))
Returns:
res(pymongo.Cursor) | scout/adapter/mongo/institute.py | def institutes(self, institute_ids=None):
"""Fetch all institutes.
Args:
institute_ids(list(str))
Returns:
res(pymongo.Cursor)
"""
query = {}
if institute_ids:
query['_id'] = {'$in': institute_ids}
LOG.debug("F... | def institutes(self, institute_ids=None):
"""Fetch all institutes.
Args:
institute_ids(list(str))
Returns:
res(pymongo.Cursor)
"""
query = {}
if institute_ids:
query['_id'] = {'$in': institute_ids}
LOG.debug("F... | [
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"pymongo",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/institute.py#L149-L162 | [
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test | match_date | Check if a string is a valid date
Args:
date(str)
Returns:
bool | scout/utils/date.py | def match_date(date):
"""Check if a string is a valid date
Args:
date(str)
Returns:
bool
"""
date_pattern = re.compile("^(19|20)\d\d[- /.](0[1-9]|1[012])[- /.](0[1-9]|[12][0-9]|3[01])")
if re.match(date_pattern, date):
return True
return False | def match_date(date):
"""Check if a string is a valid date
Args:
date(str)
Returns:
bool
"""
date_pattern = re.compile("^(19|20)\d\d[- /.](0[1-9]|1[012])[- /.](0[1-9]|[12][0-9]|3[01])")
if re.match(date_pattern, date):
return True
return False | [
"Check",
"if",
"a",
"string",
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"valid",
"date"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/date.py#L4-L17 | [
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")",
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"return",
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"retur... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_date | Return a datetime object if there is a valid date
Raise exception if date is not valid
Return todays date if no date where added
Args:
date(str)
date_format(str)
Returns:
date_obj(datetime.datetime) | scout/utils/date.py | def get_date(date, date_format = None):
"""Return a datetime object if there is a valid date
Raise exception if date is not valid
Return todays date if no date where added
Args:
date(str)
date_format(str)
Returns:
date_obj(datetime.datetime)
... | def get_date(date, date_format = None):
"""Return a datetime object if there is a valid date
Raise exception if date is not valid
Return todays date if no date where added
Args:
date(str)
date_format(str)
Returns:
date_obj(datetime.datetime)
... | [
"Return",
"a",
"datetime",
"object",
"if",
"there",
"is",
"a",
"valid",
"date"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/date.py#L19-L50 | [
"def",
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"datetime",
".",
"datetime",
".",
"strptime",
"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | hpo_genes | Export a list of genes based on hpo terms | scout/commands/export/hpo.py | def hpo_genes(context, hpo_term):
"""Export a list of genes based on hpo terms"""
LOG.info("Running scout export hpo_genes")
adapter = context.obj['adapter']
header = ["#Gene_id\tCount"]
if not hpo_term:
LOG.warning("Please use at least one hpo term")
context.abort()
for l... | def hpo_genes(context, hpo_term):
"""Export a list of genes based on hpo terms"""
LOG.info("Running scout export hpo_genes")
adapter = context.obj['adapter']
header = ["#Gene_id\tCount"]
if not hpo_term:
LOG.warning("Please use at least one hpo term")
context.abort()
for l... | [
"Export",
"a",
"list",
"of",
"genes",
"based",
"on",
"hpo",
"terms"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/export/hpo.py#L10-L25 | [
"def",
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"[",
"\"#Gene_id\\tCount\"",
"]",
"if",
"not",
"hp... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_genes | Parse transcript information and get the gene information from there.
Use hgnc_id as identifier for genes and ensembl transcript id to identify transcripts
Args:
transcripts(iterable(dict))
Returns:
genes (list(dict)): A list with dictionaries that represents genes | scout/parse/variant/gene.py | def parse_genes(transcripts):
"""Parse transcript information and get the gene information from there.
Use hgnc_id as identifier for genes and ensembl transcript id to identify transcripts
Args:
transcripts(iterable(dict))
Returns:
genes (list(dict)): A list with dictionaries th... | def parse_genes(transcripts):
"""Parse transcript information and get the gene information from there.
Use hgnc_id as identifier for genes and ensembl transcript id to identify transcripts
Args:
transcripts(iterable(dict))
Returns:
genes (list(dict)): A list with dictionaries th... | [
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"and",
"ensembl",
"transcript",
"id",
"to",
"identify",
"transcripts",
"Args",
":",
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... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/gene.py#L16-L114 | [
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"genes",
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_rank_score | Parse the rank score
Args:
rank_score_entry(str): The raw rank score entry
case_id(str)
Returns:
rank_score(float) | scout/parse/variant/rank_score.py | def parse_rank_score(rank_score_entry, case_id):
"""Parse the rank score
Args:
rank_score_entry(str): The raw rank score entry
case_id(str)
Returns:
rank_score(float)
"""
rank_score = None
if rank_score_entry:
for family_info in rank_score_en... | def parse_rank_score(rank_score_entry, case_id):
"""Parse the rank score
Args:
rank_score_entry(str): The raw rank score entry
case_id(str)
Returns:
rank_score(float)
"""
rank_score = None
if rank_score_entry:
for family_info in rank_score_en... | [
"Parse",
"the",
"rank",
"score"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/rank_score.py#L3-L19 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | user | Add a user to the database. | scout/commands/load/user.py | def user(context, institute_id, user_name, user_mail, admin):
"""Add a user to the database."""
adapter = context.obj['adapter']
institutes = []
for institute in institute_id:
institute_obj = adapter.institute(institute_id=institute)
if not institute_obj:
LOG.warning("Insti... | def user(context, institute_id, user_name, user_mail, admin):
"""Add a user to the database."""
adapter = context.obj['adapter']
institutes = []
for institute in institute_id:
institute_obj = adapter.institute(institute_id=institute)
if not institute_obj:
LOG.warning("Insti... | [
"Add",
"a",
"user",
"to",
"the",
"database",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/load/user.py#L24-L51 | [
"def",
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"ins... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_transcripts | Parse transcript information from VCF variants
Args:
raw_transcripts(iterable(dict)): An iterable with raw transcript
information
Yields:
transcript(dict) A dictionary with transcript information | scout/parse/variant/transcript.py | def parse_transcripts(raw_transcripts, allele=None):
"""Parse transcript information from VCF variants
Args:
raw_transcripts(iterable(dict)): An iterable with raw transcript
information
Yields:
transcript(dict) A dictionary with transcript informat... | def parse_transcripts(raw_transcripts, allele=None):
"""Parse transcript information from VCF variants
Args:
raw_transcripts(iterable(dict)): An iterable with raw transcript
information
Yields:
transcript(dict) A dictionary with transcript informat... | [
"Parse",
"transcript",
"information",
"from",
"VCF",
"variants"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/transcript.py#L9-L201 | [
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"transcript",
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"# There can be several functional annotations for one variant",
"functional_annotations",
"=",
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | check_connection | Check if a connection could be made to the mongo process specified
Args:
host(str)
port(int)
username(str)
password(str)
authdb (str): database to to for authentication
max_delay(int): Number of milliseconds to wait for connection
Returns:
bool: If conne... | scout/adapter/utils.py | def check_connection(host='localhost', port=27017, username=None, password=None,
authdb=None, max_delay=1):
"""Check if a connection could be made to the mongo process specified
Args:
host(str)
port(int)
username(str)
password(str)
authdb (str): data... | def check_connection(host='localhost', port=27017, username=None, password=None,
authdb=None, max_delay=1):
"""Check if a connection could be made to the mongo process specified
Args:
host(str)
port(int)
username(str)
password(str)
authdb (str): data... | [
"Check",
"if",
"a",
"connection",
"could",
"be",
"made",
"to",
"the",
"mongo",
"process",
"specified"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/utils.py#L17-L50 | [
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"#uri looks like:",
"#mongodb://[username:pas... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | MongoDB.init_app | Initialize from flask | scout/server/extensions.py | def init_app(self, app):
"""Initialize from flask"""
uri = app.config.get("MONGO_URI", None)
db_name = app.config.get("MONGO_DBNAME", 'scout')
try:
client = get_connection(
host = app.config.get("MONGO_HOST", 'localhost'),
por... | def init_app(self, app):
"""Initialize from flask"""
uri = app.config.get("MONGO_URI", None)
db_name = app.config.get("MONGO_DBNAME", 'scout')
try:
client = get_connection(
host = app.config.get("MONGO_HOST", 'localhost'),
por... | [
"Initialize",
"from",
"flask"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/extensions.py#L43-L63 | [
"def",
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | institutes | Display a list of all user institutes. | scout/server/blueprints/institutes/views.py | def institutes():
"""Display a list of all user institutes."""
institute_objs = user_institutes(store, current_user)
institutes = []
for ins_obj in institute_objs:
sanger_recipients = []
for user_mail in ins_obj.get('sanger_recipients',[]):
user_obj = store.user(user_mail)
... | def institutes():
"""Display a list of all user institutes."""
institute_objs = user_institutes(store, current_user)
institutes = []
for ins_obj in institute_objs:
sanger_recipients = []
for user_mail in ins_obj.get('sanger_recipients',[]):
user_obj = store.user(user_mail)
... | [
"Display",
"a",
"list",
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"user",
"institutes",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/institutes/views.py#L17-L41 | [
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"i... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | load_delivery_report | Load a delivery report into a case in the database
If the report already exists the function will exit.
If the user want to load a report that is already in the database
'update' has to be 'True'
Args:
adapter (MongoAdapter): Connection to the database
report_path (string): P... | scout/load/report.py | def load_delivery_report(adapter: MongoAdapter,
report_path: str,
case_id: str,
update: bool = False):
""" Load a delivery report into a case in the database
If the report already exists the function will exit.
If the user want to l... | def load_delivery_report(adapter: MongoAdapter,
report_path: str,
case_id: str,
update: bool = False):
""" Load a delivery report into a case in the database
If the report already exists the function will exit.
If the user want to l... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/load/report.py#L10-L48 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | build_transcript | Build a transcript object
These represents the transcripts that are parsed from the VCF, not
the transcript definitions that are collected from ensembl.
Args:
transcript(dict): Parsed transcript information
Returns:
transcript_obj(dict) | scout/build/variant/transcript.py | def build_transcript(transcript, build='37'):
"""Build a transcript object
These represents the transcripts that are parsed from the VCF, not
the transcript definitions that are collected from ensembl.
Args:
transcript(dict): Parsed transcript information
Returns:
... | def build_transcript(transcript, build='37'):
"""Build a transcript object
These represents the transcripts that are parsed from the VCF, not
the transcript definitions that are collected from ensembl.
Args:
transcript(dict): Parsed transcript information
Returns:
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test | UserHandler.update_user | Update an existing user.
Args:
user_obj(dict)
Returns:
updated_user(dict) | scout/adapter/mongo/user.py | def update_user(self, user_obj):
"""Update an existing user.
Args:
user_obj(dict)
Returns:
updated_user(dict)
"""
LOG.info("Updating user %s", user_obj['_id'])
updated_user = self.user_collection.find_one_... | def update_user(self, user_obj):
"""Update an existing user.
Args:
user_obj(dict)
Returns:
updated_user(dict)
"""
LOG.info("Updating user %s", user_obj['_id'])
updated_user = self.user_collection.find_one_... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/user.py#L14-L30 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | UserHandler.add_user | Add a user object to the database
Args:
user_obj(scout.models.User): A dictionary with user information
Returns:
user_info(dict): a copy of what was inserted | scout/adapter/mongo/user.py | def add_user(self, user_obj):
"""Add a user object to the database
Args:
user_obj(scout.models.User): A dictionary with user information
Returns:
user_info(dict): a copy of what was inserted
"""
LOG.info("Adding user %s to the dat... | def add_user(self, user_obj):
"""Add a user object to the database
Args:
user_obj(scout.models.User): A dictionary with user information
Returns:
user_info(dict): a copy of what was inserted
"""
LOG.info("Adding user %s to the dat... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/user.py#L32-L51 | [
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test | UserHandler.users | Return all users from the database
Args:
institute(str): A institute_id
Returns:
res(pymongo.Cursor): A cursor with users | scout/adapter/mongo/user.py | def users(self, institute=None):
"""Return all users from the database
Args:
institute(str): A institute_id
Returns:
res(pymongo.Cursor): A cursor with users
"""
query = {}
if institute:
LOG.info("Fetch... | def users(self, institute=None):
"""Return all users from the database
Args:
institute(str): A institute_id
Returns:
res(pymongo.Cursor): A cursor with users
"""
query = {}
if institute:
LOG.info("Fetch... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | UserHandler.user | Fetch a user from the database.
Args:
email(str)
Returns:
user_obj(dict) | scout/adapter/mongo/user.py | def user(self, email):
"""Fetch a user from the database.
Args:
email(str)
Returns:
user_obj(dict)
"""
LOG.info("Fetching user %s", email)
user_obj = self.user_collection.find_one({'_id': email})
return us... | def user(self, email):
"""Fetch a user from the database.
Args:
email(str)
Returns:
user_obj(dict)
"""
LOG.info("Fetching user %s", email)
user_obj = self.user_collection.find_one({'_id': email})
return us... | [
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] | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | UserHandler.delete_user | Delete a user from the database
Args:
email(str)
Returns:
user_obj(dict) | scout/adapter/mongo/user.py | def delete_user(self, email):
"""Delete a user from the database
Args:
email(str)
Returns:
user_obj(dict)
"""
LOG.info("Deleting user %s", email)
user_obj = self.user_collection.delete_one({'_id': email})
ret... | def delete_user(self, email):
"""Delete a user from the database
Args:
email(str)
Returns:
user_obj(dict)
"""
LOG.info("Deleting user %s", email)
user_obj = self.user_collection.delete_one({'_id': email})
ret... | [
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"user_... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | build_compound | Build a compound
Args:
compound(dict)
Returns:
compound_obj(dict)
dict(
# This must be the document_id for this variant
variant = str, # required=True
# This is the variant id
display_name = str, # required
combined_score = float, # requ... | scout/build/variant/compound.py | def build_compound(compound):
"""Build a compound
Args:
compound(dict)
Returns:
compound_obj(dict)
dict(
# This must be the document_id for this variant
variant = str, # required=True
# This is the variant id
display_name = str, # required
... | def build_compound(compound):
"""Build a compound
Args:
compound(dict)
Returns:
compound_obj(dict)
dict(
# This must be the document_id for this variant
variant = str, # required=True
# This is the variant id
display_name = str, # required
... | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | remote_static | Stream *large* static files with special requirements. | scout/server/blueprints/alignviewers/views.py | def remote_static():
"""Stream *large* static files with special requirements."""
file_path = request.args.get('file')
range_header = request.headers.get('Range', None)
if not range_header and file_path.endswith('.bam'):
return abort(500)
new_resp = send_file_partial(file_path)
return ... | def remote_static():
"""Stream *large* static files with special requirements."""
file_path = request.args.get('file')
range_header = request.headers.get('Range', None)
if not range_header and file_path.endswith('.bam'):
return abort(500)
new_resp = send_file_partial(file_path)
return ... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/alignviewers/views.py#L16-L25 | [
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test | pileup | Visualize BAM alignments. | scout/server/blueprints/alignviewers/views.py | def pileup():
"""Visualize BAM alignments."""
vcf_file = request.args.get('vcf')
bam_files = request.args.getlist('bam')
bai_files = request.args.getlist('bai')
samples = request.args.getlist('sample')
alignments = [{'bam': bam, 'bai': bai, 'sample': sample}
for bam, bai, sampl... | def pileup():
"""Visualize BAM alignments."""
vcf_file = request.args.get('vcf')
bam_files = request.args.getlist('bam')
bai_files = request.args.getlist('bai')
samples = request.args.getlist('sample')
alignments = [{'bam': bam, 'bai': bai, 'sample': sample}
for bam, bai, sampl... | [
"Visualize",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/alignviewers/views.py#L29-L64 | [
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test | igv | Visualize BAM alignments using igv.js (https://github.com/igvteam/igv.js) | scout/server/blueprints/alignviewers/views.py | def igv():
"""Visualize BAM alignments using igv.js (https://github.com/igvteam/igv.js)"""
chrom = request.args.get('contig')
if chrom == 'MT':
chrom = 'M'
start = request.args.get('start')
stop = request.args.get('stop')
locus = "chr{0}:{1}-{2}".format(chrom,start,stop)
LOG.debug(... | def igv():
"""Visualize BAM alignments using igv.js (https://github.com/igvteam/igv.js)"""
chrom = request.args.get('contig')
if chrom == 'MT':
chrom = 'M'
start = request.args.get('start')
stop = request.args.get('stop')
locus = "chr{0}:{1}-{2}".format(chrom,start,stop)
LOG.debug(... | [
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test | build_disease_term | Build a disease phenotype object
Args:
disease_info(dict): Dictionary with phenotype information
alias_genes(dict): {
<alias_symbol>: {
'true': hgnc_id or None,
'ids': [<hgnc_id>, ...]}}
... | scout/build/disease.py | def build_disease_term(disease_info, alias_genes={}):
"""Build a disease phenotype object
Args:
disease_info(dict): Dictionary with phenotype information
alias_genes(dict): {
<alias_symbol>: {
'true': hgnc_id or None,
... | def build_disease_term(disease_info, alias_genes={}):
"""Build a disease phenotype object
Args:
disease_info(dict): Dictionary with phenotype information
alias_genes(dict): {
<alias_symbol>: {
'true': hgnc_id or None,
... | [
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"... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/build/disease.py#L7-L79 | [
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test | load_exons | Load all the exons
Transcript information is from ensembl.
Check that the transcript that the exon belongs to exists in the database
Args:
adapter(MongoAdapter)
exon_lines(iterable): iterable with ensembl exon lines
build(str)
ensembl_transcripts(dict): Existing ensembl... | scout/load/exon.py | def load_exons(adapter, exon_lines, build='37', ensembl_genes=None):
"""Load all the exons
Transcript information is from ensembl.
Check that the transcript that the exon belongs to exists in the database
Args:
adapter(MongoAdapter)
exon_lines(iterable): iterable with ensembl exon ... | def load_exons(adapter, exon_lines, build='37', ensembl_genes=None):
"""Load all the exons
Transcript information is from ensembl.
Check that the transcript that the exon belongs to exists in the database
Args:
adapter(MongoAdapter)
exon_lines(iterable): iterable with ensembl exon ... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_variant | Return a parsed variant
Get all the necessary information to build a variant object
Args:
variant(cyvcf2.Variant)
case(dict)
variant_type(str): 'clinical' or 'research'
rank_results_header(list)
vep_header(list)
individual_positions(dict): Explain what posit... | scout/parse/variant/variant.py | def parse_variant(variant, case, variant_type='clinical',
rank_results_header=None, vep_header=None,
individual_positions=None, category=None):
"""Return a parsed variant
Get all the necessary information to build a variant object
Args:
variant(cyvcf2.Variant)... | def parse_variant(variant, case, variant_type='clinical',
rank_results_header=None, vep_header=None,
individual_positions=None, category=None):
"""Return a parsed variant
Get all the necessary information to build a variant object
Args:
variant(cyvcf2.Variant)... | [
"Return",
"a",
"parsed",
"variant"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/variant.py#L26-L297 | [
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test | compounds | Update all compounds for a case | scout/commands/update/compounds.py | def compounds(context, case_id):
"""
Update all compounds for a case
"""
adapter = context.obj['adapter']
LOG.info("Running scout update compounds")
# Check if the case exists
case_obj = adapter.case(case_id)
if not case_obj:
LOG.warning("Case %s could not be found", case_id... | def compounds(context, case_id):
"""
Update all compounds for a case
"""
adapter = context.obj['adapter']
LOG.info("Running scout update compounds")
# Check if the case exists
case_obj = adapter.case(case_id)
if not case_obj:
LOG.warning("Case %s could not be found", case_id... | [
"Update",
"all",
"compounds",
"for",
"a",
"case"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/update/compounds.py#L12-L29 | [
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"case",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | add_gene_links | Update a gene object with links
Args:
gene_obj(dict)
build(int)
Returns:
gene_obj(dict): gene_obj updated with many links | scout/server/links.py | def add_gene_links(gene_obj, build=37):
"""Update a gene object with links
Args:
gene_obj(dict)
build(int)
Returns:
gene_obj(dict): gene_obj updated with many links
"""
try:
build = int(build)
except ValueError:
build = 37
# Add links that use the hg... | def add_gene_links(gene_obj, build=37):
"""Update a gene object with links
Args:
gene_obj(dict)
build(int)
Returns:
gene_obj(dict): gene_obj updated with many links
"""
try:
build = int(build)
except ValueError:
build = 37
# Add links that use the hg... | [
"Update",
"a",
"gene",
"object",
"with",
"links"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/links.py#L3-L49 | [
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"'hgnc_id'"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | hgnc | Query the hgnc aliases | scout/commands/query/query_command.py | def hgnc(ctx, hgnc_symbol, hgnc_id, build):
"""
Query the hgnc aliases
"""
adapter = ctx.obj['adapter']
if not (hgnc_symbol or hgnc_id):
log.warning("Please provide a hgnc symbol or hgnc id")
ctx.abort()
if hgnc_id:
result = adapter.hgnc_gene(hgnc_id, build=build)
... | def hgnc(ctx, hgnc_symbol, hgnc_id, build):
"""
Query the hgnc aliases
"""
adapter = ctx.obj['adapter']
if not (hgnc_symbol or hgnc_id):
log.warning("Please provide a hgnc symbol or hgnc id")
ctx.abort()
if hgnc_id:
result = adapter.hgnc_gene(hgnc_id, build=build)
... | [
"Query",
"the",
"hgnc",
"aliases"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/query/query_command.py#L21-L52 | [
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"\"Please provide a... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_hgnc_line | Parse an hgnc formated line
Args:
line(list): A list with hgnc gene info
header(list): A list with the header info
Returns:
hgnc_info(dict): A dictionary with the relevant info | scout/parse/hgnc.py | def parse_hgnc_line(line, header):
"""Parse an hgnc formated line
Args:
line(list): A list with hgnc gene info
header(list): A list with the header info
Returns:
hgnc_info(dict): A dictionary with the relevant info
"""
hgnc_gene = {}
line = line.rstr... | def parse_hgnc_line(line, header):
"""Parse an hgnc formated line
Args:
line(list): A list with hgnc gene info
header(list): A list with the header info
Returns:
hgnc_info(dict): A dictionary with the relevant info
"""
hgnc_gene = {}
line = line.rstr... | [
"Parse",
"an",
"hgnc",
"formated",
"line"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/hgnc.py#L7-L85 | [
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")",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_hgnc_genes | Parse lines with hgnc formated genes
This is designed to take a dump with genes from HGNC.
This is downloaded from:
ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
Args:
lines(iterable(str)): An iterable with HGNC formated genes
Yields:
... | scout/parse/hgnc.py | def parse_hgnc_genes(lines):
"""Parse lines with hgnc formated genes
This is designed to take a dump with genes from HGNC.
This is downloaded from:
ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
Args:
lines(iterable(str)): An iterable with HGN... | def parse_hgnc_genes(lines):
"""Parse lines with hgnc formated genes
This is designed to take a dump with genes from HGNC.
This is downloaded from:
ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
Args:
lines(iterable(str)): An iterable with HGN... | [
"Parse",
"lines",
"with",
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"formated",
"genes"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/hgnc.py#L88-L108 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.create_submission | Create an open clinvar submission for a user and an institute
Args:
user_id(str): a user ID
institute_id(str): an institute ID
returns:
submission(obj): an open clinvar submission object | scout/adapter/mongo/clinvar.py | def create_submission(self, user_id, institute_id):
"""Create an open clinvar submission for a user and an institute
Args:
user_id(str): a user ID
institute_id(str): an institute ID
returns:
submission(obj): an open clinvar submission object... | def create_submission(self, user_id, institute_id):
"""Create an open clinvar submission for a user and an institute
Args:
user_id(str): a user ID
institute_id(str): an institute ID
returns:
submission(obj): an open clinvar submission object... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L13-L31 | [
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"'institute_id'"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.delete_submission | Deletes a Clinvar submission object, along with all associated clinvar objects (variants and casedata)
Args:
submission_id(str): the ID of the submission to be deleted
Returns:
deleted_objects(int): the number of associated objects removed (variants and/or cased... | scout/adapter/mongo/clinvar.py | def delete_submission(self, submission_id):
"""Deletes a Clinvar submission object, along with all associated clinvar objects (variants and casedata)
Args:
submission_id(str): the ID of the submission to be deleted
Returns:
deleted_objects(int): the numb... | def delete_submission(self, submission_id):
"""Deletes a Clinvar submission object, along with all associated clinvar objects (variants and casedata)
Args:
submission_id(str): the ID of the submission to be deleted
Returns:
deleted_objects(int): the numb... | [
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"(",
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"and",
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")"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L34-L68 | [
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"find_one",
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"'_id'"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.get_open_clinvar_submission | Retrieve the database id of an open clinvar submission for a user and institute,
if none is available then create a new submission and return it
Args:
user_id(str): a user ID
institute_id(str): an institute ID
Returns:
submission(obj) : ... | scout/adapter/mongo/clinvar.py | def get_open_clinvar_submission(self, user_id, institute_id):
"""Retrieve the database id of an open clinvar submission for a user and institute,
if none is available then create a new submission and return it
Args:
user_id(str): a user ID
institute_id(str)... | def get_open_clinvar_submission(self, user_id, institute_id):
"""Retrieve the database id of an open clinvar submission for a user and institute,
if none is available then create a new submission and return it
Args:
user_id(str): a user ID
institute_id(str)... | [
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"is",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L71-L92 | [
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"query",
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"(",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.update_clinvar_id | saves an official clinvar submission ID in a clinvar submission object
Args:
clinvar_id(str): a string with a format: SUB[0-9]. It is obtained from clinvar portal when starting a new submission
submission_id(str): submission_id(str) : id of the submission to be updated
... | scout/adapter/mongo/clinvar.py | def update_clinvar_id(self, clinvar_id, submission_id ):
"""saves an official clinvar submission ID in a clinvar submission object
Args:
clinvar_id(str): a string with a format: SUB[0-9]. It is obtained from clinvar portal when starting a new submission
submission_id... | def update_clinvar_id(self, clinvar_id, submission_id ):
"""saves an official clinvar submission ID in a clinvar submission object
Args:
clinvar_id(str): a string with a format: SUB[0-9]. It is obtained from clinvar portal when starting a new submission
submission_id... | [
"saves",
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"submission",
"ID",
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"a",
"clinvar",
"submission",
"object"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L95-L106 | [
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","... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.get_clinvar_id | Returns the official Clinvar submission ID for a submission object
Args:
submission_id(str): submission_id(str) : id of the submission
Returns:
clinvar_subm_id(str): a string with a format: SUB[0-9]. It is obtained from clinvar portal when starting a new submiss... | scout/adapter/mongo/clinvar.py | def get_clinvar_id(self, submission_id):
"""Returns the official Clinvar submission ID for a submission object
Args:
submission_id(str): submission_id(str) : id of the submission
Returns:
clinvar_subm_id(str): a string with a format: SUB[0-9]. It is obta... | def get_clinvar_id(self, submission_id):
"""Returns the official Clinvar submission ID for a submission object
Args:
submission_id(str): submission_id(str) : id of the submission
Returns:
clinvar_subm_id(str): a string with a format: SUB[0-9]. It is obta... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L109-L121 | [
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"submissi... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.add_to_submission | Adds submission_objects to clinvar collection and update the coresponding submission object with their id
Args:
submission_id(str) : id of the submission to be updated
submission_objects(tuple): a tuple of 2 elements coresponding to a list of variants and a list of case data... | scout/adapter/mongo/clinvar.py | def add_to_submission(self, submission_id, submission_objects):
"""Adds submission_objects to clinvar collection and update the coresponding submission object with their id
Args:
submission_id(str) : id of the submission to be updated
submission_objects(tuple): a tup... | def add_to_submission(self, submission_id, submission_objects):
"""Adds submission_objects to clinvar collection and update the coresponding submission object with their id
Args:
submission_id(str) : id of the submission to be updated
submission_objects(tuple): a tup... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L124-L157 | [
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",",
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"# Insert variant submission_objects into clinvar collection... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.update_clinvar_submission_status | Set a clinvar submission ID to 'closed'
Args:
submission_id(str): the ID of the clinvar submission to close
Return
updated_submission(obj): the submission object with a 'closed' status | scout/adapter/mongo/clinvar.py | def update_clinvar_submission_status(self, user_id, submission_id, status):
"""Set a clinvar submission ID to 'closed'
Args:
submission_id(str): the ID of the clinvar submission to close
Return
updated_submission(obj): the submission object with a 'close... | def update_clinvar_submission_status(self, user_id, submission_id, status):
"""Set a clinvar submission ID to 'closed'
Args:
submission_id(str): the ID of the clinvar submission to close
Return
updated_submission(obj): the submission object with a 'close... | [
"Set",
"a",
"clinvar",
"submission",
"ID",
"to",
"closed"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L160-L188 | [
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",",
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":",
"# just close the s... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.clinvar_submissions | Collect all open and closed clinvar submission created by a user for an institute
Args:
user_id(str): a user ID
institute_id(str): an institute ID
Returns:
submissions(list): a list of clinvar submission objects | scout/adapter/mongo/clinvar.py | def clinvar_submissions(self, user_id, institute_id):
"""Collect all open and closed clinvar submission created by a user for an institute
Args:
user_id(str): a user ID
institute_id(str): an institute ID
Returns:
submissions(list): a list... | def clinvar_submissions(self, user_id, institute_id):
"""Collect all open and closed clinvar submission created by a user for an institute
Args:
user_id(str): a user ID
institute_id(str): an institute ID
Returns:
submissions(list): a list... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L191-L226 | [
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"query"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.clinvar_objs | Collects a list of objects from the clinvar collection (variants of case data) as specified by the key_id in the clinvar submission
Args:
submission_id(str): the _id key of a clinvar submission
key_id(str) : either 'variant_data' or 'case_data'. It's a key in a clinvar_submi... | scout/adapter/mongo/clinvar.py | def clinvar_objs(self, submission_id, key_id):
"""Collects a list of objects from the clinvar collection (variants of case data) as specified by the key_id in the clinvar submission
Args:
submission_id(str): the _id key of a clinvar submission
key_id(str) : either 'v... | def clinvar_objs(self, submission_id, key_id):
"""Collects a list of objects from the clinvar collection (variants of case data) as specified by the key_id in the clinvar submission
Args:
submission_id(str): the _id key of a clinvar submission
key_id(str) : either 'v... | [
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"as",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L229-L250 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | ClinVarHandler.delete_clinvar_object | Remove a variant object from clinvar database and update the relative submission object
Args:
object_id(str) : the id of an object to remove from clinvar_collection database collection (a variant of a case)
object_type(str) : either 'variant_data' or 'case_data'. It's a key ... | scout/adapter/mongo/clinvar.py | def delete_clinvar_object(self, object_id, object_type, submission_id):
"""Remove a variant object from clinvar database and update the relative submission object
Args:
object_id(str) : the id of an object to remove from clinvar_collection database collection (a variant of a case)
... | def delete_clinvar_object(self, object_id, object_type, submission_id):
"""Remove a variant object from clinvar database and update the relative submission object
Args:
object_id(str) : the id of an object to remove from clinvar_collection database collection (a variant of a case)
... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L253-L298 | [
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test | ClinVarHandler.case_to_clinVars | Get all variants included in clinvar submissions for a case
Args:
case_id(str): a case _id
Returns:
submission_variants(dict): keys are variant ids and values are variant submission objects | scout/adapter/mongo/clinvar.py | def case_to_clinVars(self, case_id):
"""Get all variants included in clinvar submissions for a case
Args:
case_id(str): a case _id
Returns:
submission_variants(dict): keys are variant ids and values are variant submission objects
"""
query = dict(case_i... | def case_to_clinVars(self, case_id):
"""Get all variants included in clinvar submissions for a case
Args:
case_id(str): a case _id
Returns:
submission_variants(dict): keys are variant ids and values are variant submission objects
"""
query = dict(case_i... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/adapter/mongo/clinvar.py#L301-L317 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_hpo_phenotype | Parse hpo phenotype
Args:
hpo_line(str): A iterable with hpo phenotype lines
Yields:
hpo_info(dict) | scout/parse/hpo.py | def parse_hpo_phenotype(hpo_line):
"""Parse hpo phenotype
Args:
hpo_line(str): A iterable with hpo phenotype lines
Yields:
hpo_info(dict)
"""
hpo_line = hpo_line.rstrip().split('\t')
hpo_info = {}
hpo_info['hpo_id'] = hpo_line[0]
hpo_info['descri... | def parse_hpo_phenotype(hpo_line):
"""Parse hpo phenotype
Args:
hpo_line(str): A iterable with hpo phenotype lines
Yields:
hpo_info(dict)
"""
hpo_line = hpo_line.rstrip().split('\t')
hpo_info = {}
hpo_info['hpo_id'] = hpo_line[0]
hpo_info['descri... | [
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"["... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_hpo_gene | Parse hpo gene information
Args:
hpo_line(str): A iterable with hpo phenotype lines
Yields:
hpo_info(dict) | scout/parse/hpo.py | def parse_hpo_gene(hpo_line):
"""Parse hpo gene information
Args:
hpo_line(str): A iterable with hpo phenotype lines
Yields:
hpo_info(dict)
"""
if not len(hpo_line) > 3:
return {}
hpo_line = hpo_line.rstrip().split('\t')
hpo_info = {}
hpo... | def parse_hpo_gene(hpo_line):
"""Parse hpo gene information
Args:
hpo_line(str): A iterable with hpo phenotype lines
Yields:
hpo_info(dict)
"""
if not len(hpo_line) > 3:
return {}
hpo_line = hpo_line.rstrip().split('\t')
hpo_info = {}
hpo... | [
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test | parse_hpo_disease | Parse hpo disease line
Args:
hpo_line(str) | scout/parse/hpo.py | def parse_hpo_disease(hpo_line):
"""Parse hpo disease line
Args:
hpo_line(str)
"""
hpo_line = hpo_line.rstrip().split('\t')
hpo_info = {}
disease = hpo_line[0].split(':')
hpo_info['source'] = disease[0]
hpo_info['disease_nr'] = int(disease[1])
hpo_info['hgnc... | def parse_hpo_disease(hpo_line):
"""Parse hpo disease line
Args:
hpo_line(str)
"""
hpo_line = hpo_line.rstrip().split('\t')
hpo_info = {}
disease = hpo_line[0].split(':')
hpo_info['source'] = disease[0]
hpo_info['disease_nr'] = int(disease[1])
hpo_info['hgnc... | [
"Parse",
"hpo",
"disease",
"line",
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":",
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")"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/hpo.py#L42-L64 | [
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test | parse_hpo_phenotypes | Parse hpo phenotypes
Group the genes that a phenotype is associated to in 'genes'
Args:
hpo_lines(iterable(str)): A file handle to the hpo phenotypes file
Returns:
hpo_terms(dict): A dictionary with hpo_ids as keys and terms as values
{
<hpo_id>: {... | scout/parse/hpo.py | def parse_hpo_phenotypes(hpo_lines):
"""Parse hpo phenotypes
Group the genes that a phenotype is associated to in 'genes'
Args:
hpo_lines(iterable(str)): A file handle to the hpo phenotypes file
Returns:
hpo_terms(dict): A dictionary with hpo_ids as keys and terms as v... | def parse_hpo_phenotypes(hpo_lines):
"""Parse hpo phenotypes
Group the genes that a phenotype is associated to in 'genes'
Args:
hpo_lines(iterable(str)): A file handle to the hpo phenotypes file
Returns:
hpo_terms(dict): A dictionary with hpo_ids as keys and terms as v... | [
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"... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/hpo.py#L66-L101 | [
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test | parse_hpo_diseases | Parse hpo disease phenotypes
Args:
hpo_lines(iterable(str))
Returns:
diseases(dict): A dictionary with mim numbers as keys | scout/parse/hpo.py | def parse_hpo_diseases(hpo_lines):
"""Parse hpo disease phenotypes
Args:
hpo_lines(iterable(str))
Returns:
diseases(dict): A dictionary with mim numbers as keys
"""
diseases = {}
LOG.info("Parsing hpo diseases...")
for index, line in enumerate(hp... | def parse_hpo_diseases(hpo_lines):
"""Parse hpo disease phenotypes
Args:
hpo_lines(iterable(str))
Returns:
diseases(dict): A dictionary with mim numbers as keys
"""
diseases = {}
LOG.info("Parsing hpo diseases...")
for index, line in enumerate(hp... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/hpo.py#L103-L146 | [
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"inde... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_hpo_to_genes | Parse the map from hpo term to hgnc symbol
Args:
lines(iterable(str)):
Yields:
hpo_to_gene(dict): A dictionary with information on how a term map to a hgnc symbol | scout/parse/hpo.py | def parse_hpo_to_genes(hpo_lines):
"""Parse the map from hpo term to hgnc symbol
Args:
lines(iterable(str)):
Yields:
hpo_to_gene(dict): A dictionary with information on how a term map to a hgnc symbol
"""
for line in hpo_lines:
if line.startswith('#') or len(line) <... | def parse_hpo_to_genes(hpo_lines):
"""Parse the map from hpo term to hgnc symbol
Args:
lines(iterable(str)):
Yields:
hpo_to_gene(dict): A dictionary with information on how a term map to a hgnc symbol
"""
for line in hpo_lines:
if line.startswith('#') or len(line) <... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_hpo_genes | Parse HPO gene information
Args:
hpo_lines(iterable(str))
Returns:
diseases(dict): A dictionary with hgnc symbols as keys | scout/parse/hpo.py | def parse_hpo_genes(hpo_lines):
"""Parse HPO gene information
Args:
hpo_lines(iterable(str))
Returns:
diseases(dict): A dictionary with hgnc symbols as keys
"""
LOG.info("Parsing HPO genes ...")
genes = {}
for index, line in enumerate(hpo_lines):... | def parse_hpo_genes(hpo_lines):
"""Parse HPO gene information
Args:
hpo_lines(iterable(str))
Returns:
diseases(dict): A dictionary with hgnc symbols as keys
"""
LOG.info("Parsing HPO genes ...")
genes = {}
for index, line in enumerate(hpo_lines):... | [
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"=="... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_incomplete_penetrance_genes | Get a set with all genes that have incomplete penetrance according to HPO
Args:
hpo_lines(iterable(str))
Returns:
incomplete_penetrance_genes(set): A set with the hgnc symbols of all
genes with incomplete penetrance | scout/parse/hpo.py | def get_incomplete_penetrance_genes(hpo_lines):
"""Get a set with all genes that have incomplete penetrance according to HPO
Args:
hpo_lines(iterable(str))
Returns:
incomplete_penetrance_genes(set): A set with the hgnc symbols of all
genes... | def get_incomplete_penetrance_genes(hpo_lines):
"""Get a set with all genes that have incomplete penetrance according to HPO
Args:
hpo_lines(iterable(str))
Returns:
incomplete_penetrance_genes(set): A set with the hgnc symbols of all
genes... | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_hpo_obo | Parse a .obo formated hpo line | scout/parse/hpo.py | def parse_hpo_obo(hpo_lines):
"""Parse a .obo formated hpo line"""
term = {}
for line in hpo_lines:
if len(line) == 0:
continue
line = line.rstrip()
# New term starts with [Term]
if line == '[Term]':
if term:
yield term
term... | def parse_hpo_obo(hpo_lines):
"""Parse a .obo formated hpo line"""
term = {}
for line in hpo_lines:
if len(line) == 0:
continue
line = line.rstrip()
# New term starts with [Term]
if line == '[Term]':
if term:
yield term
term... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/hpo.py#L237-L267 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | genes | Render seach box for genes. | scout/server/blueprints/genes/views.py | def genes():
"""Render seach box for genes."""
query = request.args.get('query', '')
if '|' in query:
hgnc_id = int(query.split(' | ', 1)[0])
return redirect(url_for('.gene', hgnc_id=hgnc_id))
gene_q = store.all_genes().limit(20)
return dict(genes=gene_q) | def genes():
"""Render seach box for genes."""
query = request.args.get('query', '')
if '|' in query:
hgnc_id = int(query.split(' | ', 1)[0])
return redirect(url_for('.gene', hgnc_id=hgnc_id))
gene_q = store.all_genes().limit(20)
return dict(genes=gene_q) | [
"Render",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/genes/views.py#L13-L20 | [
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test | gene | Render information about a gene. | scout/server/blueprints/genes/views.py | def gene(hgnc_id=None, hgnc_symbol=None):
"""Render information about a gene."""
if hgnc_symbol:
query = store.hgnc_genes(hgnc_symbol)
if query.count() == 1:
hgnc_id = query.first()['hgnc_id']
else:
return redirect(url_for('.genes', query=hgnc_symbol))
try:
... | def gene(hgnc_id=None, hgnc_symbol=None):
"""Render information about a gene."""
if hgnc_symbol:
query = store.hgnc_genes(hgnc_symbol)
if query.count() == 1:
hgnc_id = query.first()['hgnc_id']
else:
return redirect(url_for('.genes', query=hgnc_symbol))
try:
... | [
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"=",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | api_genes | Return JSON data about genes. | scout/server/blueprints/genes/views.py | def api_genes():
"""Return JSON data about genes."""
query = request.args.get('query')
json_out = controllers.genes_to_json(store, query)
return jsonify(json_out) | def api_genes():
"""Return JSON data about genes."""
query = request.args.get('query')
json_out = controllers.genes_to_json(store, query)
return jsonify(json_out) | [
"Return",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/genes/views.py#L44-L48 | [
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] | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | check_panels | Make sure that the gene panels exist in the database
Also check if the default panels are defined in gene panels
Args:
adapter(MongoAdapter)
panels(list(str)): A list with panel names
Returns:
panels_exists(bool) | scout/load/all.py | def check_panels(adapter, panels, default_panels=None):
"""Make sure that the gene panels exist in the database
Also check if the default panels are defined in gene panels
Args:
adapter(MongoAdapter)
panels(list(str)): A list with panel names
Returns:
pa... | def check_panels(adapter, panels, default_panels=None):
"""Make sure that the gene panels exist in the database
Also check if the default panels are defined in gene panels
Args:
adapter(MongoAdapter)
panels(list(str)): A list with panel names
Returns:
pa... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/load/all.py#L9-L30 | [
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"in",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | load_region | Load all variants in a region defined by a HGNC id
Args:
adapter (MongoAdapter)
case_id (str): Case id
hgnc_id (int): If all variants from a gene should be uploaded
chrom (str): If variants from coordinates should be uploaded
start (int): Start position for region
en... | scout/load/all.py | def load_region(adapter, case_id, hgnc_id=None, chrom=None, start=None, end=None):
"""Load all variants in a region defined by a HGNC id
Args:
adapter (MongoAdapter)
case_id (str): Case id
hgnc_id (int): If all variants from a gene should be uploaded
chrom (str): If variants fro... | def load_region(adapter, case_id, hgnc_id=None, chrom=None, start=None, end=None):
"""Load all variants in a region defined by a HGNC id
Args:
adapter (MongoAdapter)
case_id (str): Case id
hgnc_id (int): If all variants from a gene should be uploaded
chrom (str): If variants fro... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/load/all.py#L33-L87 | [
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test | load_scout | Load a new case from a Scout config.
Args:
adapter(MongoAdapter)
config(dict): loading info
ped(Iterable(str)): Pedigree ingformation
update(bool): If existing case should be updated | scout/load/all.py | def load_scout(adapter, config, ped=None, update=False):
"""Load a new case from a Scout config.
Args:
adapter(MongoAdapter)
config(dict): loading info
ped(Iterable(str)): Pedigree ingformation
update(bool): If existing case should be updated
"""
log... | def load_scout(adapter, config, ped=None, update=False):
"""Load a new case from a Scout config.
Args:
adapter(MongoAdapter)
config(dict): loading info
ped(Iterable(str)): Pedigree ingformation
update(bool): If existing case should be updated
"""
log... | [
"Load",
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"case",
"from",
"a",
"Scout",
"config",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/load/all.py#L90-L105 | [
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test | templated | Template decorator.
Ref: http://flask.pocoo.org/docs/patterns/viewdecorators/ | scout/server/utils.py | def templated(template=None):
"""Template decorator.
Ref: http://flask.pocoo.org/docs/patterns/viewdecorators/
"""
def decorator(f):
@wraps(f)
def decorated_function(*args, **kwargs):
template_name = template
if template_name is None:
template_nam... | def templated(template=None):
"""Template decorator.
Ref: http://flask.pocoo.org/docs/patterns/viewdecorators/
"""
def decorator(f):
@wraps(f)
def decorated_function(*args, **kwargs):
template_name = template
if template_name is None:
template_nam... | [
"Template",
"decorator",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/utils.py#L7-L25 | [
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"if",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | institute_and_case | Fetch insitiute and case objects. | scout/server/utils.py | def institute_and_case(store, institute_id, case_name=None):
"""Fetch insitiute and case objects."""
institute_obj = store.institute(institute_id)
if institute_obj is None and institute_id != 'favicon.ico':
flash("Can't find institute: {}".format(institute_id), 'warning')
return abort(404)
... | def institute_and_case(store, institute_id, case_name=None):
"""Fetch insitiute and case objects."""
institute_obj = store.institute(institute_id)
if institute_obj is None and institute_id != 'favicon.ico':
flash("Can't find institute: {}".format(institute_id), 'warning')
return abort(404)
... | [
"Fetch",
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"objects",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/utils.py#L33-L59 | [
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"'favicon.ico'",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | user_institutes | Preprocess institute objects. | scout/server/utils.py | def user_institutes(store, login_user):
"""Preprocess institute objects."""
if login_user.is_admin:
institutes = store.institutes()
else:
institutes = [store.institute(inst_id) for inst_id in login_user.institutes]
return institutes | def user_institutes(store, login_user):
"""Preprocess institute objects."""
if login_user.is_admin:
institutes = store.institutes()
else:
institutes = [store.institute(inst_id) for inst_id in login_user.institutes]
return institutes | [
"Preprocess",
"institute",
"objects",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/utils.py#L62-L69 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_hgnc_id | Get the hgnc id for a gene
The proprity order will be
1. if there is a hgnc id this one will be choosen
2. if the hgnc symbol matches a genes proper hgnc symbol
3. if the symbol ony matches aliases on several genes one will be
choosen at random
Args:
gene... | scout/utils/hgnc_id.py | def get_hgnc_id(gene_info, adapter):
"""Get the hgnc id for a gene
The proprity order will be
1. if there is a hgnc id this one will be choosen
2. if the hgnc symbol matches a genes proper hgnc symbol
3. if the symbol ony matches aliases on several genes one will be
choos... | def get_hgnc_id(gene_info, adapter):
"""Get the hgnc id for a gene
The proprity order will be
1. if there is a hgnc id this one will be choosen
2. if the hgnc symbol matches a genes proper hgnc symbol
3. if the symbol ony matches aliases on several genes one will be
choos... | [
"Get",
"the",
"hgnc",
"id",
"for",
"a",
"gene"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/hgnc_id.py#L1-L34 | [
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"true_id... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | panel | Update a panel in the database | scout/commands/update/panel.py | def panel(context, panel, version, update_date, update_version):
"""
Update a panel in the database
"""
adapter = context.obj['adapter']
# Check that the panel exists
panel_obj = adapter.gene_panel(panel, version=version)
if not panel_obj:
LOG.warning("Panel %s (version %s) could n... | def panel(context, panel, version, update_date, update_version):
"""
Update a panel in the database
"""
adapter = context.obj['adapter']
# Check that the panel exists
panel_obj = adapter.gene_panel(panel, version=version)
if not panel_obj:
LOG.warning("Panel %s (version %s) could n... | [
"Update",
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"in",
"the",
"database"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/update/panel.py#L30-L57 | [
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test | diseases | Update disease terms in mongo database. | scout/commands/update/disease.py | def diseases(context, api_key):
"""
Update disease terms in mongo database.
"""
adapter = context.obj['adapter']
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key to load the omim gene pan... | def diseases(context, api_key):
"""
Update disease terms in mongo database.
"""
adapter = context.obj['adapter']
# Fetch the omim information
api_key = api_key or context.obj.get('omim_api_key')
if not api_key:
LOG.warning("Please provide a omim api key to load the omim gene pan... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/update/disease.py#L25-L52 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | load_hpo | Load the hpo terms and hpo diseases into database
Args:
adapter(MongoAdapter)
disease_lines(iterable(str)): These are the omim genemap2 information
hpo_lines(iterable(str))
disease_lines(iterable(str))
hpo_gene_lines(iterable(str)) | scout/load/hpo.py | def load_hpo(adapter, disease_lines, hpo_disease_lines=None, hpo_lines=None, hpo_gene_lines=None):
"""Load the hpo terms and hpo diseases into database
Args:
adapter(MongoAdapter)
disease_lines(iterable(str)): These are the omim genemap2 information
hpo_lines(iterable(str))
... | def load_hpo(adapter, disease_lines, hpo_disease_lines=None, hpo_lines=None, hpo_gene_lines=None):
"""Load the hpo terms and hpo diseases into database
Args:
adapter(MongoAdapter)
disease_lines(iterable(str)): These are the omim genemap2 information
hpo_lines(iterable(str))
... | [
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"gene... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | load_hpo_terms | Load the hpo terms into the database
Parse the hpo lines, build the objects and add them to the database
Args:
adapter(MongoAdapter)
hpo_lines(iterable(str))
hpo_gene_lines(iterable(str)) | scout/load/hpo.py | def load_hpo_terms(adapter, hpo_lines=None, hpo_gene_lines=None, alias_genes=None):
"""Load the hpo terms into the database
Parse the hpo lines, build the objects and add them to the database
Args:
adapter(MongoAdapter)
hpo_lines(iterable(str))
hpo_gene_lines(iterable(str))... | def load_hpo_terms(adapter, hpo_lines=None, hpo_gene_lines=None, alias_genes=None):
"""Load the hpo terms into the database
Parse the hpo lines, build the objects and add them to the database
Args:
adapter(MongoAdapter)
hpo_lines(iterable(str))
hpo_gene_lines(iterable(str))... | [
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"hpo_lines"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | load_disease_terms | Load the omim phenotypes into the database
Parse the phenotypes from genemap2.txt and find the associated hpo terms
from ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt.
Args:
adapter(MongoAdapter)
genemap_lines(iterable(str))
genes(dict): Dictionary with all ge... | scout/load/hpo.py | def load_disease_terms(adapter, genemap_lines, genes=None, hpo_disease_lines=None):
"""Load the omim phenotypes into the database
Parse the phenotypes from genemap2.txt and find the associated hpo terms
from ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt.
Args:
adapter(Mon... | def load_disease_terms(adapter, genemap_lines, genes=None, hpo_disease_lines=None):
"""Load the omim phenotypes into the database
Parse the phenotypes from genemap2.txt and find the associated hpo terms
from ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt.
Args:
adapter(Mon... | [
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"genes_by_... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_frequencies | Add the frequencies to a variant
Frequencies are parsed either directly from keys in info fieds or from the
transcripts is they are annotated there.
Args:
variant(cyvcf2.Variant): A parsed vcf variant
transcripts(iterable(dict)): Parsed transcripts
Returns:
frequencies(dict): ... | scout/parse/variant/frequency.py | def parse_frequencies(variant, transcripts):
"""Add the frequencies to a variant
Frequencies are parsed either directly from keys in info fieds or from the
transcripts is they are annotated there.
Args:
variant(cyvcf2.Variant): A parsed vcf variant
transcripts(iterable(dict)): Parsed t... | def parse_frequencies(variant, transcripts):
"""Add the frequencies to a variant
Frequencies are parsed either directly from keys in info fieds or from the
transcripts is they are annotated there.
Args:
variant(cyvcf2.Variant): A parsed vcf variant
transcripts(iterable(dict)): Parsed t... | [
"Add",
"the",
"frequencies",
"to",
"a",
"variant"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/frequency.py#L2-L95 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_frequency | Parse any frequency from the info dict
Args:
variant(cyvcf2.Variant)
info_key(str)
Returns:
frequency(float): or None if frequency does not exist | scout/parse/variant/frequency.py | def parse_frequency(variant, info_key):
"""Parse any frequency from the info dict
Args:
variant(cyvcf2.Variant)
info_key(str)
Returns:
frequency(float): or None if frequency does not exist
"""
raw_annotation = variant.INFO.get(info_key)
raw_annotation = None if raw_anno... | def parse_frequency(variant, info_key):
"""Parse any frequency from the info dict
Args:
variant(cyvcf2.Variant)
info_key(str)
Returns:
frequency(float): or None if frequency does not exist
"""
raw_annotation = variant.INFO.get(info_key)
raw_annotation = None if raw_anno... | [
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"dict"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/frequency.py#L98-L111 | [
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"="... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
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