INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
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Get information about a case from archive. | 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': [],
... |
Migrate case information from archive. | 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... |
Update all information that was manually annotated from a old instance. | 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... |
Upload research variants to cases | 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
"... |
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 hgnc_lines ( iterable ( str )): Lines wit... | 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... |
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. | 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 ... |
Show all hpo terms in the database | 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... |
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 | 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... |
Flask app factory function. | 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)
# ... |
Configure Flask extensions. | 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... |
Register Flask blueprints. | 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... |
Setup logging of error/ exceptions to email. | 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 coverage related extensions. | 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
... |
Show all alias symbols and how they map to ids | 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... |
Build a panel_gene object Args: gene_info ( dict ) Returns: gene_obj ( dict ) panel_gene = dict ( hgnc_id = int # required symbol = str | 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... |
Build a gene_panel object | 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... |
Export variants which have been verified for an institute and write them to an excel file. | 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... |
Export causatives for a collaborator in. vcf format | 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... |
Get vcf entry from variant object | 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:
... |
Start the web server. | 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... |
Generate an md5 - key from a list of arguments. | 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):
... |
Setup via Flask. | 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 connection to database. | 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... |
Create indexes for the database | 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() |
Setup a scout database. | 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 demo instance. This instance will be populated with a case a gene panel and some variants. | 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']... |
Setup scout instances. | 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
... |
Show all institutes in the database | 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:
... |
Parse the genetic models entry of a vcf | 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(',... |
Show all gene panels in the database | 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... |
Add a institute to the database | 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... |
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
... |
Featch a single institute from the backend | 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.... |
Fetch all institutes. Args: institute_ids ( list ( str )) Returns: res ( pymongo. Cursor ) | 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... |
Check if a string is a valid date | 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 |
Return a datetime object if there is a valid date | 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)
... |
Export a list of genes based on hpo terms | 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... |
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 )) | 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... |
Parse the rank score | 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... |
Add a user to the database. | 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... |
Parse transcript information from VCF variants | 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... |
Check if a connection could be made to the mongo process specified | 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... |
Initialize from flask | 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... |
Display a list of all user institutes. | 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)
... |
Load a delivery report into a case in the database | 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... |
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 ) | 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:
... |
Update an existing user. Args: user_obj ( dict ) Returns: updated_user ( dict ) | 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_... |
Add a user object to the database | 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... |
Return all users from the database Args: institute ( str ): A institute_id Returns: res ( pymongo. Cursor ): A cursor with users | 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... |
Fetch a user from the database. Args: email ( str ) Returns: user_obj ( dict ) | 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... |
Delete a user from the database Args: email ( str ) Returns: user_obj ( dict ) | 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... |
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 # required rank_score = float not_loaded = bool genes = [ { hgnc_id: int hgnc_symbo... | 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
... |
Stream * large * static files with special requirements. | 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 ... |
Visualize BAM alignments. | 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 BAM alignments using igv. js ( https:// github. com/ igvteam/ igv. js ) | 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(... |
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 >... ] }} Returns: disease_obj ( dict ): Formated for mongodb disease_term = dict ( _id = str # Same as disease_id disease_id = str # requi... | 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,
... |
Load all the exons Transcript information is from ensembl. Check that the transcript that the exon belongs to exists in the database | 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 ... |
Return a parsed 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)... |
Update all compounds for a case | 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 a gene object with links | 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... |
Query the hgnc aliases | 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)
... |
Parse an hgnc formated line | 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 lines with hgnc formated genes | 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... |
Create an open clinvar submission for a user and an institute Args: user_id ( str ): a user ID institute_id ( str ): an institute ID | 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... |
Deletes a Clinvar submission object along with all associated clinvar objects ( variants and casedata ) | 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... |
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 | 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)... |
saves an official clinvar submission ID in a clinvar submission object | 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... |
Returns the official Clinvar submission ID for a submission object | 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... |
Adds submission_objects to clinvar collection and update the coresponding submission object with their id | 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... |
Set a clinvar submission ID to closed | 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... |
Collect all open and closed clinvar submission created by a user for an institute | 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... |
Collects a list of objects from the clinvar collection ( variants of case data ) as specified by the key_id in the clinvar submission | 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... |
Remove a variant object from clinvar database and update the relative submission object | 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)
... |
Get all variants included in clinvar submissions for a case | 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... |
Parse hpo phenotype Args: hpo_line ( str ): A iterable with hpo phenotype lines Yields: hpo_info ( dict ) | 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... |
Parse hpo gene information Args: hpo_line ( str ): A iterable with hpo phenotype lines Yields: hpo_info ( dict ) | 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... |
Parse hpo disease line Args: hpo_line ( str ) | 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 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 >: { hpo_id: str description: str hgnc_symbols: list ( str ) # [ <hgn... | 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... |
Parse hpo disease phenotypes Args: hpo_lines ( iterable ( str )) Returns: diseases ( dict ): A dictionary with mim numbers as keys | 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... |
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 | 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) <... |
Parse HPO gene information Args: hpo_lines ( iterable ( str )) Returns: diseases ( dict ): A dictionary with hgnc symbols as keys | 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):... |
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 | 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... |
Parse a. obo formated hpo line | 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... |
Render seach box for genes. | 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 information about a gene. | 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:
... |
Return JSON data about genes. | 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) |
Make sure that the gene panels exist in the database Also check if the default panels are defined in gene panels | 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... |
Load all variants in a region defined by a HGNC id | 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... |
Load a new case from a Scout config. | 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... |
Template decorator. | 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... |
Fetch insitiute and case objects. | 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)
... |
Preprocess institute objects. | 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 |
Get the hgnc id for a gene | 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... |
Update a panel in the database | 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 disease terms in mongo database. | 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... |
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 )) | 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))
... |
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))... |
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. | 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... |
Add the frequencies to a variant | 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... |
Parse any frequency from the info dict | 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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