def gene_variants(store,
pymongo_cursor,
variant_count,
institute_id,
page=1,
per_page=50):
"""Pre-process list of variants."""
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = pymongo_cursor.skip(skip_count).limit(per_page)
my_institutes = set(inst["_id"]
for inst in user_institutes(store, current_user))
variants = []
for variant_obj in variant_res:
# Populate variant case_display_name
variant_case_obj = store.case(case_id=variant_obj["case_id"])
if not variant_case_obj:
# A variant with missing case was encountered
continue
case_display_name = variant_case_obj.get("display_name")
variant_obj["case_display_name"] = case_display_name
# hide other institutes for now
other_institutes = set([variant_case_obj.get("owner")])
other_institutes.update(set(variant_case_obj.get("collaborators", [])))
if my_institutes.isdisjoint(other_institutes):
# If the user does not have access to the information we skip it
continue
genome_build = get_genome_build(variant_case_obj)
variant_genes = variant_obj.get("genes")
gene_object = update_HGNC_symbols(store, variant_genes, genome_build)
# Populate variant HGVS and predictions
variant_genes = variant_obj.get("genes")
hgvs_c = []
hgvs_p = []
if variant_genes is not None:
for gene_obj in variant_genes:
hgnc_id = gene_obj["hgnc_id"]
gene_symbol = gene(store, hgnc_id)["symbol"]
gene_symbols = [gene_symbol]
# gather HGVS info from gene transcripts
(hgvs_nucleotide, hgvs_protein) = get_hgvs(gene_obj)
hgvs_c.append(hgvs_nucleotide)
hgvs_p.append(hgvs_protein)
if len(gene_symbols) == 1:
variant_obj["hgvs"] = hgvs_str(gene_symbols, hgvs_p, hgvs_c)
# populate variant predictions for display
variant_obj.update(predictions(variant_genes))
variants.append(variant_obj)
return {"variants": variants, "more_variants": more_variants}
def variant_export_genes_info(store, gene_list):
"""Adds gene info to a list of fields corresponding to a variant to be exported.
Args:
gene_list(list) A list of gene objects contained in the variant
Returns:
gene_info(list) A list of gene-relates string info
"""
gene_ids = []
gene_names = []
hgvs_c = []
gene_info = []
for gene_obj in gene_list:
hgnc_id = gene_obj["hgnc_id"]
gene_name = gene(store, hgnc_id)["symbol"]
gene_ids.append(hgnc_id)
gene_names.append(gene_name)
hgvs_nucleotide = "-"
# gather HGVS info from gene transcripts
transcripts_list = gene_obj.get("transcripts")
for transcript_obj in transcripts_list:
if (transcript_obj.get("is_canonical") is not None
and transcript_obj.get("is_canonical") is True):
hgvs_nucleotide = str(
transcript_obj.get("coding_sequence_name"))
hgvs_c.append(hgvs_nucleotide)
gene_info.append(";".join(str(x) for x in gene_ids))
gene_info.append(";".join(str(x) for x in gene_names))
gene_info.append(";".join(str(x) for x in hgvs_c))
return gene_info
def variant_export_lines(store, case_obj, variants_query):
"""Get variants info to be exported to file, one list (line) per variant.
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variants_query: a list of variant objects, each one is a dictionary
Returns:
export_variants: a list of strings. Each string of the list corresponding to the fields
of a variant to be exported to file, separated by comma
"""
export_variants = []
for variant in variants_query:
variant_line = []
position = variant['position']
change = variant['reference']+'>'+variant['alternative']
variant_line.append(variant['rank_score'])
variant_line.append(variant['chromosome'])
variant_line.append(position)
variant_line.append(change)
variant_line.append('_'.join([str(position), change]))
# gather gene info:
gene_list = variant.get('genes') #this is a list of gene objects
gene_ids = []
gene_names = []
hgvs_c = []
# if variant is in genes
if len(gene_list) > 0:
for gene_obj in gene_list:
hgnc_id = gene_obj['hgnc_id']
gene_name = gene(store, hgnc_id)['symbol']
gene_ids.append(hgnc_id)
gene_names.append(gene_name)
hgvs_nucleotide = '-'
# gather HGVS info from gene transcripts
transcripts_list = gene_obj.get('transcripts')
for transcript_obj in transcripts_list:
if transcript_obj.get('is_canonical') and transcript_obj.get('is_canonical') is True:
hgvs_nucleotide = str(transcript_obj.get('coding_sequence_name'))
hgvs_c.append(hgvs_nucleotide)
variant_line.append(';'.join( str(x) for x in gene_ids))
variant_line.append(';'.join( str(x) for x in gene_names))
variant_line.append(';'.join( str(x) for x in hgvs_c))
else:
while i < 4:
variant_line.append('-') # instead of gene ids
i = i+1
variant_gts = variant['samples'] # list of coverage and gt calls for case samples
for individual in case_obj['individuals']:
for variant_gt in variant_gts:
if individual['individual_id'] == variant_gt['sample_id']:
# gather coverage info
variant_line.append(variant_gt['allele_depths'][0]) # AD reference
variant_line.append(variant_gt['allele_depths'][1]) # AD alternate
# gather genotype quality info
variant_line.append(variant_gt['genotype_quality'])
variant_line = [str(i) for i in variant_line]
export_variants.append(",".join(variant_line))
return export_variants
def variant_export_lines(store, case_obj, variants_query):
"""Get variants info to be exported to file, one list (line) per variant.
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variants_query: a list of variant objects, each one is a dictionary
Returns:
export_variants: a list of strings. Each string of the list corresponding to the fields
of a variant to be exported to file, separated by comma
"""
export_variants = []
for variant in variants_query:
variant_line = []
position = variant["position"]
change = variant["reference"] + ">" + variant["alternative"]
variant_line.append(variant["rank_score"])
variant_line.append(variant["chromosome"])
variant_line.append(position)
variant_line.append(change)
variant_line.append("_".join([str(position), change]))
# gather gene info:
gene_list = variant.get("genes") # this is a list of gene objects
gene_ids = []
gene_names = []
hgvs_c = []
# if variant is in genes
if len(gene_list) > 0:
for gene_obj in gene_list:
hgnc_id = gene_obj["hgnc_id"]
gene_name = gene(store, hgnc_id)["symbol"]
gene_ids.append(hgnc_id)
gene_names.append(gene_name)
hgvs_nucleotide = "-"
# gather HGVS info from gene transcripts
transcripts_list = gene_obj.get("transcripts")
for transcript_obj in transcripts_list:
if (transcript_obj.get("is_canonical")
and transcript_obj.get("is_canonical") is True):
hgvs_nucleotide = str(
transcript_obj.get("coding_sequence_name"))
hgvs_c.append(hgvs_nucleotide)
variant_line.append(";".join(str(x) for x in gene_ids))
variant_line.append(";".join(str(x) for x in gene_names))
variant_line.append(";".join(str(x) for x in hgvs_c))
else:
i = 0
while i < 4:
variant_line.append("-") # instead of gene ids
i = i + 1
variant_gts = variant[
"samples"] # list of coverage and gt calls for case samples
for individual in case_obj["individuals"]:
for variant_gt in variant_gts:
if individual["individual_id"] == variant_gt["sample_id"]:
# gather coverage info
variant_line.append(
variant_gt["allele_depths"][0]) # AD reference
variant_line.append(
variant_gt["allele_depths"][1]) # AD alternate
# gather genotype quality info
variant_line.append(variant_gt["genotype_quality"])
variant_line = [str(i) for i in variant_line]
export_variants.append(",".join(variant_line))
return export_variants
def gene_variants(store, variants_query, page=1, per_page=50):
"""Pre-process list of variants."""
variant_count = variants_query.count()
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = variants_query.skip(skip_count).limit(per_page)
my_institutes = list(inst['_id']
for inst in user_institutes(store, current_user))
variants = []
for variant_obj in variant_res:
# hide other institutes for now
if variant_obj['institute'] not in my_institutes:
LOG.warning("Institute {} not allowed.".format(
variant_obj['institute']))
continue
# Populate variant case_display_name
variant_case_obj = store.case(case_id=variant_obj['case_id'])
if not variant_case_obj:
# A variant with missing case was encountered
continue
case_display_name = variant_case_obj.get('display_name')
variant_obj['case_display_name'] = case_display_name
genome_build = variant_case_obj.get('genome_build', '37')
if genome_build not in ['37', '38']:
genome_build = '37'
# Update the HGNC symbols if they are not set
variant_genes = variant_obj.get('genes')
if variant_genes is not None:
for gene_obj in variant_genes:
# If there is no hgnc id there is nothin we can do
if not gene_obj['hgnc_id']:
continue
# Else we collect the gene object and check the id
if gene_obj.get('hgnc_symbol') is None or gene_obj.get(
'description') is None:
hgnc_gene = store.hgnc_gene(gene_obj['hgnc_id'],
build=genome_build)
if not hgnc_gene:
continue
gene_obj['hgnc_symbol'] = hgnc_gene['hgnc_symbol']
gene_obj['description'] = hgnc_gene['description']
# Populate variant HGVS and predictions
gene_ids = []
gene_symbols = []
hgvs_c = []
hgvs_p = []
variant_genes = variant_obj.get('genes')
if variant_genes is not None:
functional_annotation = ''
for gene_obj in variant_genes:
hgnc_id = gene_obj['hgnc_id']
gene_symbol = gene(store, hgnc_id)['symbol']
gene_ids.append(hgnc_id)
gene_symbols.append(gene_symbol)
hgvs_nucleotide = '-'
# gather HGVS info from gene transcripts
transcripts_list = gene_obj.get('transcripts')
for transcript_obj in transcripts_list:
if transcript_obj.get(
'is_canonical'
) and transcript_obj.get('is_canonical') is True:
hgvs_nucleotide = str(
transcript_obj.get('coding_sequence_name'))
hgvs_protein = str(
transcript_obj.get('protein_sequence_name'))
hgvs_c.append(hgvs_nucleotide)
hgvs_p.append(hgvs_protein)
if len(gene_symbols) == 1:
if (hgvs_p[0] != "None"):
hgvs = hgvs_p[0]
elif (hgvs_c[0] != "None"):
hgvs = hgvs_c[0]
else:
hgvs = "-"
variant_obj['hgvs'] = hgvs
# populate variant predictions for display
variant_obj.update(get_predictions(variant_genes))
variants.append(variant_obj)
return {
'variants': variants,
'more_variants': more_variants,
}
def gene_variants(store, variants_query, institute_id, page=1, per_page=50):
"""Pre-process list of variants."""
# We need to call variants_collection.count_documents here
variant_count = variants_query.count()
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = variants_query.skip(skip_count).limit(per_page)
my_institutes = set(inst["_id"]
for inst in user_institutes(store, current_user))
variants = []
for variant_obj in variant_res:
# Populate variant case_display_name
variant_case_obj = store.case(case_id=variant_obj["case_id"])
if not variant_case_obj:
# A variant with missing case was encountered
continue
case_display_name = variant_case_obj.get("display_name")
variant_obj["case_display_name"] = case_display_name
# hide other institutes for now
other_institutes = set([variant_case_obj.get("owner")])
other_institutes.update(set(variant_case_obj.get("collaborators", [])))
if my_institutes.isdisjoint(other_institutes):
# If the user does not have access to the information we skip it
continue
genome_build = variant_case_obj.get("genome_build", "37")
if genome_build not in ["37", "38"]:
genome_build = "37"
# Update the HGNC symbols if they are not set
variant_genes = variant_obj.get("genes")
if variant_genes is not None:
for gene_obj in variant_genes:
# If there is no hgnc id there is nothin we can do
if not gene_obj["hgnc_id"]:
continue
# Else we collect the gene object and check the id
if (gene_obj.get("hgnc_symbol") is None
or gene_obj.get("description") is None):
hgnc_gene = store.hgnc_gene(gene_obj["hgnc_id"],
build=genome_build)
if not hgnc_gene:
continue
gene_obj["hgnc_symbol"] = hgnc_gene["hgnc_symbol"]
gene_obj["description"] = hgnc_gene["description"]
# Populate variant HGVS and predictions
gene_ids = []
gene_symbols = []
hgvs_c = []
hgvs_p = []
variant_genes = variant_obj.get("genes")
if variant_genes is not None:
functional_annotation = ""
for gene_obj in variant_genes:
hgnc_id = gene_obj["hgnc_id"]
gene_symbol = gene(store, hgnc_id)["symbol"]
gene_ids.append(hgnc_id)
gene_symbols.append(gene_symbol)
hgvs_nucleotide = "-"
# gather HGVS info from gene transcripts
transcripts_list = gene_obj.get("transcripts")
for transcript_obj in transcripts_list:
if (transcript_obj.get("is_canonical")
and transcript_obj.get("is_canonical") is True):
hgvs_nucleotide = str(
transcript_obj.get("coding_sequence_name"))
hgvs_protein = str(
transcript_obj.get("protein_sequence_name"))
hgvs_c.append(hgvs_nucleotide)
hgvs_p.append(hgvs_protein)
if len(gene_symbols) == 1:
if hgvs_p[0] != "None":
hgvs = hgvs_p[0]
elif hgvs_c[0] != "None":
hgvs = hgvs_c[0]
else:
hgvs = "-"
variant_obj["hgvs"] = hgvs
# populate variant predictions for display
variant_obj.update(predictions(variant_genes))
variants.append(variant_obj)
return {"variants": variants, "more_variants": more_variants}
def gene_variants(store, variants_query, page=1, per_page=50):
"""Pre-process list of variants."""
variant_count = variants_query.count()
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = variants_query.skip(skip_count).limit(per_page)
my_institutes = list(inst['_id'] for inst in user_institutes(store, current_user))
variants = []
for variant_obj in variant_res:
# hide other institutes for now
if variant_obj['institute'] not in my_institutes:
LOG.warning("Institute {} not allowed.".format(variant_obj['institute']))
continue
# Populate variant case_display_name
variant_case_obj = store.case(case_id=variant_obj['case_id'])
if not variant_case_obj:
# A variant with missing case was encountered
continue
case_display_name = variant_case_obj.get('display_name')
variant_obj['case_display_name'] = case_display_name
genome_build = variant_case_obj.get('genome_build', '37')
if genome_build not in ['37','38']:
genome_build = '37'
# Update the HGNC symbols if they are not set
variant_genes = variant_obj.get('genes')
if variant_genes is not None:
for gene_obj in variant_genes:
# If there is no hgnc id there is nothin we can do
if not gene_obj['hgnc_id']:
continue
# Else we collect the gene object and check the id
if gene_obj.get('hgnc_symbol') is None or gene_obj.get('description') is None:
hgnc_gene = store.hgnc_gene(gene_obj['hgnc_id'], build=genome_build)
if not hgnc_gene:
continue
gene_obj['hgnc_symbol'] = hgnc_gene['hgnc_symbol']
gene_obj['description'] = hgnc_gene['description']
# Populate variant HGVS and predictions
gene_ids = []
gene_symbols = []
hgvs_c = []
hgvs_p = []
variant_genes = variant_obj.get('genes')
if variant_genes is not None:
functional_annotation = ''
for gene_obj in variant_genes:
hgnc_id = gene_obj['hgnc_id']
gene_symbol = gene(store, hgnc_id)['symbol']
gene_ids.append(hgnc_id)
gene_symbols.append(gene_symbol)
hgvs_nucleotide = '-'
# gather HGVS info from gene transcripts
transcripts_list = gene_obj.get('transcripts')
for transcript_obj in transcripts_list:
if transcript_obj.get('is_canonical') and transcript_obj.get('is_canonical') is True:
hgvs_nucleotide = str(transcript_obj.get('coding_sequence_name'))
hgvs_protein = str(transcript_obj.get('protein_sequence_name'))
hgvs_c.append(hgvs_nucleotide)
hgvs_p.append(hgvs_protein)
if len(gene_symbols) == 1:
if(hgvs_p[0] != "None"):
hgvs = hgvs_p[0]
elif(hgvs_c[0] != "None"):
hgvs = hgvs_c[0]
else:
hgvs = "-"
variant_obj['hgvs'] = hgvs
# populate variant predictions for display
variant_obj.update(get_predictions(variant_genes))
variants.append(variant_obj)
return {
'variants': variants,
'more_variants': more_variants,
}
