def gene(gene_name):
title = gene_name
tbl_color = {"LOW": 'success', "MODERATE": 'warning', "HIGH": 'danger'}
bcs = OrderedDict([("Gene", None), (title, None)])
result = list(wb_gene.filter((wb_gene.Name == gene_name) |
(wb_gene.sequence_name == gene_name) |
(wb_gene.locus == gene_name)).dicts().execute())
if len(result) != 1:
return render_template('404.html'), 404
gene_record = result[0]
# Retrieve variants
variants = WI.select().filter(
WI.CHROM == gene_record["CHROM"],
WI.gene_id == gene_record["Name"]).dicts().execute()
# Retrieve mappings
mapping_set = mapping.select(mapping, trait, report) \
.join(trait) \
.join(report) \
.where((gene_record["CHROM"] == mapping.chrom) &
(report.release == 0) &
(gene_record["start"] >= mapping.interval_start) &
(gene_record["end"] <= mapping.interval_end)) \
.dicts() \
.execute()
return render_template('gene.html', **locals())
def gt_from_interval(chrom, start, end, var_eff):
if var_eff == "ALL":
var_eff = WI.CHROM == chrom
else:
var_eff = (WI.putative_impact << var_eff)
result = list(WI.select(WI.CHROM,
WI.POS,
WI.REF,
WI.ALT,
WI.FILTER,
WI.transcript_biotype,
WI.putative_impact,
WI.gene_name,
WI.gene_id,
WI.hgvs_p,
WI.protein_position,
WI.GT,
WI.feature_id,
WI.annotation)
.filter(WI.CHROM == chrom,
WI.POS >= start,
WI.POS <= end,
var_eff)
.limit(1000)
.dicts()
.execute())
for i in result:
i["GT"] = decode_gt(i["GT"])
return result
def variants_in_biotype(chrom, start, end):
q = list(WI.select(WI.transcript_biotype) \
.filter(WI.gene_id != "",
WI.CHROM == chrom,
WI.POS >= start,
WI.POS <= end,
WI.FILTER == "") \
.group_by(WI.variant) \
.tuples()
.execute())
q = count_column(q)
q["total"] = sum(q.values())
return q
def get_variant_count(chrom, start, end, filter=True):
"""
Return the number of variants within an interval
"""
if filter:
var_filter = (WI.FILTER == "")
else:
var_filter = (1 == 1)
return WI.select(WI.variant) \
.filter((WI.CHROM == chrom) &
(WI.POS >= start) &
(WI.POS <= end) &
(var_filter)) \
.group_by() \
.distinct().count()
def get_gene_w_impact(chrom, start, end):
"""
Return Genes with variants of given impact for a given interval
"""
q_biotype = Counter(list(WI.select(WI.transcript_biotype, WI.putative_impact) \
.filter(WI.gene_id != "",
WI.CHROM == chrom,
WI.POS >= start,
WI.POS <= end,
WI.FILTER == "") \
.group_by(WI.gene_id, WI.transcript_biotype) \
.tuples()
.execute()))
total = {"LOW": 0, "MODERATE": 0, "HIGH":0}
for k,v in zip([x[1] for x in q_biotype.keys()], q_biotype.values()):
total[k] += v
by_biotype = defaultdict(dict)
for k,v in q_biotype.items():
by_biotype[k[1]][k[0]] = v
response = {}
response["total"] = total
response.update(by_biotype)
return response
def get_gt(chrom, pos):
"""
return GT by chrom and position
"""
return decode_gt(WI.get(WI.CHROM == chrom, WI.POS == pos).GT)
