def test_parse_vep_header(variant_clinical_file): ## GIVEN a vcf object vcf_obj = VCF(variant_clinical_file) ## WHEN parsing the vep header vep_header = parse_vep_header(vcf_obj) ## THEN assert the header is returned correct assert isinstance(vep_header, list) assert vep_header assert "ALLELE" in vep_header
def test_parse_vep_header(variant_clinical_file): ## GIVEN a vcf object vcf_obj = VCF(variant_clinical_file) ## WHEN parsing the vep header vep_header = parse_vep_header(vcf_obj) ## THEN assert the header is returned correct assert isinstance(vep_header, list) assert vep_header assert 'ALLELE' in vep_header
def load_variants( self, case_obj, variant_type="clinical", category="snv", rank_threshold=None, chrom=None, start=None, end=None, gene_obj=None, build="37", ): """Load variants for a case into scout. Load the variants for a specific analysis type and category into scout. If no region is specified, load all variants above rank score threshold If region or gene is specified, load all variants from that region disregarding variant rank(if not specified) Args: case_obj(dict): A case from the scout database variant_type(str): 'clinical' or 'research'. Default: 'clinical' category(str): 'snv', 'str' or 'sv'. Default: 'snv' rank_threshold(float): Only load variants above this score. Default: 0 chrom(str): Load variants from a certain chromosome start(int): Specify the start position end(int): Specify the end position gene_obj(dict): A gene object from the database Returns: nr_inserted(int) """ # We need the institute object institute_id = self.institute(institute_id=case_obj["owner"])["_id"] nr_inserted = 0 variant_file = None if variant_type == "clinical": if category == "snv": variant_file = case_obj["vcf_files"].get("vcf_snv") elif category == "sv": variant_file = case_obj["vcf_files"].get("vcf_sv") elif category == "str": LOG.debug("Attempt to load STR VCF.") variant_file = case_obj["vcf_files"].get("vcf_str") elif category == "cancer": # Currently this implies a paired tumor normal variant_file = case_obj["vcf_files"].get("vcf_cancer") elif category == "cancer_sv": # ditto for paired tumor normal variant_file = case_obj["vcf_files"].get("vcf_cancer_sv") elif variant_type == "research": if category == "snv": variant_file = case_obj["vcf_files"].get("vcf_snv_research") elif category == "sv": variant_file = case_obj["vcf_files"].get("vcf_sv_research") elif category == "cancer": variant_file = case_obj["vcf_files"].get("vcf_cancer_research") elif category == "cancer_sv": variant_file = case_obj["vcf_files"].get( "vcf_cancer_sv_research") if not variant_file: raise SyntaxError("Vcf file does not seem to exist") # Check if there are any variants in file try: vcf_obj = VCF(variant_file) var = next(vcf_obj) except StopIteration as err: LOG.warning("Variant file %s does not include any variants", variant_file) return nr_inserted # We need to reload the file vcf_obj = VCF(variant_file) # Parse the neccessary headers from vcf file rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) if vep_header: LOG.info("Found VEP header %s", "|".join(vep_header)) # This is a dictionary to tell where ind are in vcf individual_positions = {} for i, ind in enumerate(vcf_obj.samples): individual_positions[ind] = i # Dictionary for cancer analysis sample_info = {} if category in ("cancer", "cancer_sv"): for ind in case_obj["individuals"]: if ind["phenotype"] == 2: sample_info[ind["individual_id"]] = "case" else: sample_info[ind["individual_id"]] = "control" # Check if a region scould be uploaded region = "" if gene_obj: chrom = gene_obj["chromosome"] # Add same padding as VEP start = max(gene_obj["start"] - 5000, 0) end = gene_obj["end"] + 5000 if chrom: # We want to load all variants in the region regardless of rank score rank_threshold = rank_threshold or -1000 if not (start and end): raise SyntaxError("Specify chrom start and end") region = "{0}:{1}-{2}".format(chrom, start, end) else: rank_threshold = rank_threshold or 0 variants = vcf_obj(region) try: nr_inserted = self._load_variants( variants=variants, variant_type=variant_type, case_obj=case_obj, individual_positions=individual_positions, rank_threshold=rank_threshold, institute_id=institute_id, build=build, rank_results_header=rank_results_header, vep_header=vep_header, category=category, sample_info=sample_info, ) except Exception as error: LOG.exception("unexpected error") LOG.warning("Deleting inserted variants") self.delete_variants(case_obj["_id"], variant_type) raise error self.update_variant_rank(case_obj, variant_type, category=category) return nr_inserted
def load_variants(self, case_obj, variant_type='clinical', category='snv', rank_threshold=None, chrom=None, start=None, end=None, gene_obj=None, build='37'): """Load variants for a case into scout. Load the variants for a specific analysis type and category into scout. If no region is specified, load all variants above rank score threshold If region or gene is specified, load all variants from that region disregarding variant rank(if not specified) Args: case_obj(dict): A case from the scout database variant_type(str): 'clinical' or 'research'. Default: 'clinical' category(str): 'snv', 'str' or 'sv'. Default: 'snv' rank_threshold(float): Only load variants above this score. Default: 0 chrom(str): Load variants from a certain chromosome start(int): Specify the start position end(int): Specify the end position gene_obj(dict): A gene object from the database Returns: nr_inserted(int) """ # We need the institute object institute_id = self.institute(institute_id=case_obj['owner'])['_id'] nr_inserted = 0 variant_file = None if variant_type == 'clinical': if category == 'snv': variant_file = case_obj['vcf_files'].get('vcf_snv') elif category == 'sv': variant_file = case_obj['vcf_files'].get('vcf_sv') elif category == 'str': LOG.debug('Attempt to load STR VCF.') variant_file = case_obj['vcf_files'].get('vcf_str') elif category == 'cancer': # Currently this implies a paired tumor normal variant_file = case_obj['vcf_files'].get('vcf_cancer') elif variant_type == 'research': if category == 'snv': variant_file = case_obj['vcf_files'].get('vcf_snv_research') elif category == 'sv': variant_file = case_obj['vcf_files'].get('vcf_sv_research') elif category == 'cancer': variant_file = case_obj['vcf_files'].get('vcf_cancer_research') if not variant_file: raise SyntaxError("Vcf file does not seem to exist") # Check if there are any variants in file try: vcf_obj = VCF(variant_file) var = next(vcf_obj) except StopIteration as err: LOG.warning("Variant file %s does not include any variants", variant_file) return nr_inserted # We need to reload the file vcf_obj = VCF(variant_file) # Parse the neccessary headers from vcf file rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) # This is a dictionary to tell where ind are in vcf individual_positions = {} for i, ind in enumerate(vcf_obj.samples): individual_positions[ind] = i # Dictionary for cancer analysis sample_info = {} if category == 'cancer': for ind in case_obj['individuals']: if ind['phenotype'] == 2: sample_info[ind['individual_id']] = 'case' else: sample_info[ind['individual_id']] = 'control' # Check if a region scould be uploaded region = "" if gene_obj: chrom = gene_obj['chromosome'] # Add same padding as VEP start = max(gene_obj['start'] - 5000, 0) end = gene_obj['end'] + 5000 if chrom: # We want to load all variants in the region regardless of rank score rank_threshold = rank_threshold or -1000 if not (start and end): raise SyntaxError("Specify chrom start and end") region = "{0}:{1}-{2}".format(chrom, start, end) else: rank_threshold = rank_threshold or 0 variants = vcf_obj(region) try: nr_inserted = self._load_variants( variants=variants, variant_type=variant_type, case_obj=case_obj, individual_positions=individual_positions, rank_threshold=rank_threshold, institute_id=institute_id, build=build, rank_results_header=rank_results_header, vep_header=vep_header, category=category, sample_info = sample_info ) except Exception as error: LOG.exception('unexpected error') LOG.warning("Deleting inserted variants") self.delete_variants(case_obj['_id'], variant_type) raise error self.update_variant_rank(case_obj, variant_type, category=category) return nr_inserted
def load_variants(adapter, variant_file, case_obj, variant_type='clinical', category='snv', rank_threshold=5, chrom=None, start=None, end=None): """Load all variant in variants Args: adapter(MongoAdapter) variant_file(str): Path to variant file case(Case) variant_type(str) category(str): 'snv' or 'sv' rank_threshold(int) chrom(str) start(int) end(int) """ institute_obj = adapter.institute(institute_id=case_obj['owner']) if not institute_obj: raise IntegrityError("Institute {0} does not exist in" " database.".format(case_obj['owner'])) gene_to_panels = adapter.gene_to_panels() hgncid_to_gene = adapter.hgncid_to_gene() coordinates = {} vcf_obj = VCF(variant_file) rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) # This is a dictionary to tell where ind are in vcf individual_positions = {} for i,ind in enumerate(vcf_obj.samples): individual_positions[ind] = i logger.info("Start inserting variants into database") start_insertion = datetime.now() start_five_thousand = datetime.now() nr_variants = 0 nr_inserted = 0 inserted = 1 coordinates = False if chrom: coordinates = { 'chrom': chrom, 'start': start, 'end': end } try: for nr_variants, variant in enumerate(vcf_obj): rank_score = parse_rank_score( variant.INFO.get('RankScore'), case_obj['display_name'] ) variant_obj = None add_variant = False if coordinates or (rank_score > rank_threshold): parsed_variant = parse_variant( variant=variant, case=case_obj, variant_type=variant_type, rank_results_header=rank_results_header, vep_header = vep_header, individual_positions = individual_positions ) add_variant = True # If there are coordinates the variant should be loaded if coordinates: if not check_coordinates(parsed_variant, coordinates): add_variant = False if add_variant: variant_obj = build_variant( variant=parsed_variant, institute_id=institute_obj['_id'], gene_to_panels=gene_to_panels, hgncid_to_gene=hgncid_to_gene, ) try: load_variant(adapter, variant_obj) nr_inserted += 1 except IntegrityError as error: pass if (nr_variants != 0 and nr_variants % 5000 == 0): logger.info("%s variants parsed" % str(nr_variants)) logger.info("Time to parse variants: {} ".format( datetime.now() - start_five_thousand)) start_five_thousand = datetime.now() if (nr_inserted != 0 and (nr_inserted * inserted) % (1000 * inserted) == 0): logger.info("%s variants inserted" % nr_inserted) inserted += 1 except Exception as error: if not coordinates: logger.warning("Deleting inserted variants") delete_variants(adapter, case_obj, variant_type) raise error logger.info("All variants inserted.") logger.info("Number of variants in file: {0}".format(nr_variants + 1)) logger.info("Number of variants inserted: {0}".format(nr_inserted)) logger.info("Time to insert variants:{0}".format(datetime.now() - start_insertion))
def test_compounds_region(real_populated_database, case_obj, variant_clinical_file): """When loading the variants not all variants will be loaded, only the ones that have a rank score above a treshold. This implies that some compounds will have the status 'not_loaded'=True. When loading all variants for a region then all variants should have status 'not_loaded'=False. """ adapter = real_populated_database variant_type = "clinical" category = "snv" ## GIVEN a database without any variants assert adapter.variant_collection.find_one() is None institute_obj = adapter.institute_collection.find_one() institute_id = institute_obj["_id"] ## WHEN loading variants into the database without updating compound information vcf_obj = VCF(variant_clinical_file) rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) individual_positions = {} for i, ind in enumerate(vcf_obj.samples): individual_positions[ind] = i variants = [] for i, variant in enumerate(vcf_obj): parsed_variant = parse_variant( variant=variant, case=case_obj, variant_type="clinical", rank_results_header=rank_results_header, vep_header=vep_header, individual_positions=individual_positions, category="snv", ) variant_obj = build_variant(variant=parsed_variant, institute_id=institute_id) variants.append(variant_obj) # Load all variants adapter.variant_collection.insert_many(variants) print("Nr variants: {0}".format(len(variants))) ## THEN assert that the variants does not have updated compound information nr_compounds = 0 for var in adapter.variant_collection.find(): if not var.get("compounds"): continue for comp in var["compounds"]: if "genes" in comp: assert False if "not_loaded" in comp: assert False nr_compounds += 1 assert nr_compounds > 0 ## WHEN updating all compounds for a case adapter.update_case_compounds(case_obj) hgnc_ids = set([gene["hgnc_id"] for gene in adapter.all_genes()]) nr_compounds = 0 ## THEN assert that all compounds (within the gene defenition) are updated for var in adapter.variant_collection.find(): cont = False for hgnc_id in var["hgnc_ids"]: if hgnc_id not in hgnc_ids: cont = True if cont: continue if not var.get("compounds"): continue for comp in var["compounds"]: nr_compounds += 1 if not "genes" in comp: # pp(var) assert False if not "not_loaded" in comp: assert False assert nr_compounds > 0
def load_variants(self, case_obj, variant_type='clinical', category='snv', rank_threshold=None, chrom=None, start=None, end=None, gene_obj=None, build='37'): """Load variants for a case into scout. Load the variants for a specific analysis type and category into scout. If no region is specified, load all variants above rank score threshold If region or gene is specified, load all variants from that region disregarding variant rank(if not specified) Args: case_obj(dict): A case from the scout database variant_type(str): 'clinical' or 'research'. Default: 'clinical' category(str): 'snv' or 'sv'. Default: 'snv' rank_threshold(float): Only load variants above this score. Default: 0 chrom(str): Load variants from a certain chromosome start(int): Specify the start position end(int): Specify the end position gene_obj(dict): A gene object from the database Returns: nr_inserted(int) """ # We need the institute object institute_id = self.institute(institute_id=case_obj['owner'])['_id'] variant_file = None if variant_type == 'clinical': if category == 'snv': variant_file = case_obj['vcf_files'].get('vcf_snv') elif category == 'sv': variant_file = case_obj['vcf_files'].get('vcf_sv') elif category == 'cancer': # Currently this implies a paired tumor normal variant_file = case_obj['vcf_files'].get('vcf_cancer') elif variant_type == 'research': if category == 'snv': variant_file = case_obj['vcf_files'].get('vcf_snv_research') elif category == 'sv': variant_file = case_obj['vcf_files'].get('vcf_sv_research') elif category == 'cancer': variant_file = case_obj['vcf_files'].get('vcf_cancer_research') if not variant_file: raise SyntaxError("Vcf file does not seem to exist") vcf_obj = VCF(variant_file) # Parse the neccessary headers from vcf file rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) # This is a dictionary to tell where ind are in vcf individual_positions = {} for i, ind in enumerate(vcf_obj.samples): individual_positions[ind] = i # Dictionary for cancer analysis sample_info = {} if category == 'cancer': for ind in case_obj['individuals']: if ind['phenotype'] == 2: sample_info[ind['individual_id']] = 'case' else: sample_info[ind['individual_id']] = 'control' # Check if a region scould be uploaded region = "" if gene_obj: chrom = gene_obj['chromosome'] # Add same padding as VEP start = max(gene_obj['start'] - 5000, 0) end = gene_obj['end'] + 5000 if chrom: # We want to load all variants in the region regardless of rank score rank_threshold = rank_threshold or -1000 if not (start and end): raise SyntaxError("Specify chrom start and end") region = "{0}:{1}-{2}".format(chrom, start, end) else: rank_threshold = rank_threshold or 0 variants = vcf_obj(region) try: nr_inserted = self._load_variants( variants=variants, variant_type=variant_type, case_obj=case_obj, individual_positions=individual_positions, rank_threshold=rank_threshold, institute_id=institute_id, build=build, rank_results_header=rank_results_header, vep_header=vep_header, category=category, sample_info=sample_info) except Exception as error: LOG.exception('unexpected error') LOG.warning("Deleting inserted variants") self.delete_variants(case_obj['_id'], variant_type) raise error self.update_variant_rank(case_obj, variant_type, category=category) return nr_inserted
def load_variants(self, case_obj, variant_type='clinical', category='snv', rank_threshold=None, chrom=None, start=None, end=None, gene_obj=None): """Load variants for a case into scout. Load all variants for a specific analysis type and category into scout. If no region is specified, load all variants above rank score threshold If region or gene is specified, load all variants from that region disregarding variant rank(if not specified) Args: case_obj(dict): A case from the scout database variant_type(str): 'clinical' or 'research'. Default: 'clinical' category(str): 'snv' or 'sv'. Default: 'snv' rank_threshold(float): Only load variants above this score. Default: 5 chrom(str): Load variants from a certain chromosome start(int): Specify the start position end(int): Specify the end position gene_obj(dict): A gene object from the database Returns: nr_inserted(int) """ institute_obj = self.institute(institute_id=case_obj['owner']) if not institute_obj: raise IntegrityError("Institute {0} does not exist in" " database.".format(case_obj['owner'])) gene_to_panels = self.gene_to_panels() hgncid_to_gene = self.hgncid_to_gene() variant_file = None if variant_type == 'clinical': if category == 'snv': variant_file = case_obj['vcf_files'].get('vcf_snv') elif category == 'sv': variant_file = case_obj['vcf_files'].get('vcf_sv') elif variant_type == 'research': if category == 'snv': variant_file = case_obj['vcf_files'].get('vcf_snv_research') elif category == 'sv': variant_file = case_obj['vcf_files'].get('vcf_sv_research') if not variant_file: raise SyntaxError("Vcf file does not seem to exist") vcf_obj = VCF(variant_file) # Parse the neccessary headers from vcf file rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) # This is a dictionary to tell where ind are in vcf individual_positions = {} for i,ind in enumerate(vcf_obj.samples): individual_positions[ind] = i # Check if a region scould be uploaded region = "" if gene_obj: chrom = gene_obj['chromosome'] start = gene_obj['start'] end = gene_obj['end'] if chrom: rank_threshold = rank_threshold or -100 if not (start and end): raise SyntaxError("Specify chrom start and end") region = "{0}:{1}-{2}".format(chrom, start, end) else: rank_threshold = rank_threshold or 5 logger.info("Start inserting variants into database") start_insertion = datetime.now() start_five_thousand = datetime.now() # These are the number of parsed varaints nr_variants = 0 # These are the number of variants that meet the criteria and gets # inserted nr_inserted = 0 # This is to keep track of the inserted variants inserted = 1 try: for nr_variants, variant in enumerate(vcf_obj(region)): rank_score = parse_rank_score( variant.INFO.get('RankScore'), case_obj['display_name'] ) if rank_score > rank_threshold: # Parse the vcf variant parsed_variant = parse_variant( variant=variant, case=case_obj, variant_type=variant_type, rank_results_header=rank_results_header, vep_header = vep_header, individual_positions = individual_positions ) # Build the variant object variant_obj = build_variant( variant=parsed_variant, institute_id=institute_obj['_id'], gene_to_panels=gene_to_panels, hgncid_to_gene=hgncid_to_gene, ) try: self.load_variant(variant_obj) nr_inserted += 1 except IntegrityError as error: pass if (nr_variants != 0 and nr_variants % 5000 == 0): logger.info("%s variants parsed" % str(nr_variants)) logger.info("Time to parse variants: {} ".format( datetime.now() - start_five_thousand)) start_five_thousand = datetime.now() if (nr_inserted != 0 and (nr_inserted * inserted) % (1000 * inserted) == 0): logger.info("%s variants inserted" % nr_inserted) inserted += 1 except Exception as error: logger.warning("Deleting inserted variants") self.delete_variants(case_obj['_id'], variant_type) raise error return nr_inserted
def load_variants(adapter, variant_file, case_obj, variant_type='clinical', category='snv', rank_threshold=6, chrom=None, start=None, end=None): """Load all variant in variants Args: adapter(MongoAdapter) variant_file(str): Path to variant file case(Case) variant_type(str) category(str): 'snv' or 'sv' rank_threshold(int) chrom(str) start(int) end(int) """ institute_obj = adapter.institute(institute_id=case_obj['owner']) if not institute_obj: raise IntegrityError("Institute {0} does not exist in" " database.".format(case_obj['owner'])) gene_to_panels = adapter.gene_to_panels() hgncid_to_gene = adapter.hgncid_to_gene() coordinates = {} vcf_obj = VCF(variant_file) rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) # This is a dictionary to tell where ind are in vcf individual_positions = {} for i, ind in enumerate(vcf_obj.samples): individual_positions[ind] = i LOG.info("Start inserting variants into database") start_insertion = datetime.now() start_five_thousand = datetime.now() # To get it right if the file is empty nr_variants = -1 nr_inserted = 0 inserted = 1 coordinates = False if chrom: coordinates = {'chrom': chrom, 'start': start, 'end': end} try: for nr_variants, variant in enumerate(vcf_obj): # Get the neccesary coordinates # Parse away any chr CHR prefix chrom_match = CHR_PATTERN.match(variant.CHROM) chrom = chrom_match.group(2) position = variant.POS add_variant = False # If coordinates are specified we want to upload all variants that # resides within the specified region if coordinates: if check_coordinates(chrom, position, coordinates): add_variant = True # If there are no coordinates we allways want to load MT variants elif chrom == 'MT': add_variant = True # Otherwise we need to check is rank score requirement are fulfilled else: rank_score = parse_rank_score(variant.INFO.get('RankScore'), case_obj['display_name']) if rank_score >= rank_threshold: add_variant = True variant_obj = None # Log the number of variants parsed if (nr_variants != 0 and nr_variants % 5000 == 0): LOG.info("%s variants parsed" % str(nr_variants)) LOG.info( "Time to parse variants: {} ".format(datetime.now() - start_five_thousand)) start_five_thousand = datetime.now() if not add_variant: continue ####### Here we know that the variant should be loaded ######### # We follow the scout paradigm of parse -> build -> load # Parse the variant parsed_variant = parse_variant( variant=variant, case=case_obj, variant_type=variant_type, rank_results_header=rank_results_header, vep_header=vep_header, individual_positions=individual_positions) # Build the variant object variant_obj = build_variant( variant=parsed_variant, institute_id=institute_obj['_id'], gene_to_panels=gene_to_panels, hgncid_to_gene=hgncid_to_gene, ) # Load the variant abject # We could get integrity error here since if we want to load all variants of a region # there will likely already be variants from that region loaded try: load_variant(adapter, variant_obj) nr_inserted += 1 except IntegrityError as error: pass # Log number of inserted variants if (nr_inserted != 0 and (nr_inserted * inserted) % (1000 * inserted) == 0): LOG.info("%s variants inserted" % nr_inserted) inserted += 1 except Exception as error: if not coordinates: LOG.warning("Deleting inserted variants") delete_variants(adapter, case_obj, variant_type) raise error LOG.info("All variants inserted.") LOG.info("Number of variants in file: {0}".format(nr_variants + 1)) LOG.info("Number of variants inserted: {0}".format(nr_inserted)) LOG.info("Time to insert variants:{0}".format(datetime.now() - start_insertion))
def test_compounds_region(real_populated_database, case_obj, variant_clinical_file): """When loading the variants not all variants will be loaded, only the ones that have a rank score above a treshold. This implies that some compounds will have the status 'not_loaded'=True. When loading all variants for a region then all variants should have status 'not_loaded'=False. """ adapter = real_populated_database variant_type = 'clinical' category = 'snv' ## GIVEN a database without any variants assert adapter.variant_collection.find().count() == 0 institute_obj = adapter.institute_collection.find_one() institute_id = institute_obj['_id'] ## WHEN loading variants into the database without updating compound information vcf_obj = VCF(variant_clinical_file) rank_results_header = parse_rank_results_header(vcf_obj) vep_header = parse_vep_header(vcf_obj) individual_positions = {} for i, ind in enumerate(vcf_obj.samples): individual_positions[ind] = i variants = [] for i,variant in enumerate(vcf_obj): parsed_variant = parse_variant( variant=variant, case=case_obj, variant_type='clinical', rank_results_header=rank_results_header, vep_header=vep_header, individual_positions=individual_positions, category='snv', ) variant_obj = build_variant( variant=parsed_variant, institute_id=institute_id, ) variants.append(variant_obj) # Load all variants adapter.variant_collection.insert_many(variants) print("Nr variants: {0}".format(len(variants))) ## THEN assert that the variants does not have updated compound information nr_compounds = 0 for var in adapter.variant_collection.find(): if not var.get('compounds'): continue for comp in var['compounds']: if 'genes' in comp: assert False if 'not_loaded' in comp: assert False nr_compounds += 1 assert nr_compounds > 0 ## WHEN updating all compounds for a case adapter.update_case_compounds(case_obj) hgnc_ids = set([gene['hgnc_id'] for gene in adapter.all_genes()]) nr_compounds = 0 ## THEN assert that all compounds (within the gene defenition) are updated for var in adapter.variant_collection.find(): cont = False for hgnc_id in var['hgnc_ids']: if hgnc_id not in hgnc_ids: cont = True if cont: continue if not var.get('compounds'): continue for comp in var['compounds']: nr_compounds += 1 if not 'genes' in comp: # pp(var) assert False if not 'not_loaded' in comp: assert False assert nr_compounds > 0