def run(inheritance_model, ped, vcf, min_depth, min_gq, min_kindreds,
severity):
from cyvcf2 import VCF, Writer
vcf = VCF(vcf, samples="-")
annos = {}
if "ANN" in vcf:
desc = vcf["ANN"]["Description"]
parts = [
x.strip("\"'") for x in re.split("\s*\|\s*",
desc.split(":", 1)[1].strip('" '))
]
annos["ANN"] = desc
if "EFF" in vcf:
desc = vcf["EFF"]["Description"]
parts = [
x.strip(" [])'(\"")
for x in re.split("\||\(",
desc.split(":", 1)[1].strip())
]
annos["EFF"] = parts
if "CSQ" in vcf:
desc = vcf["CSQ"]["Description"]
parts = [
x.strip(" [])'(\"")
for x in re.split("\||\(",
desc.split(":", 1)[1].strip())
]
annos["CSQ"] = parts
vcf.update(id="inheritance",
type="String",
number="1",
description="inheritance stuffs")
out = Writer("-", vcf)
vcf_order = dict((n, i) for i, n in (enumerate(vcf.samples)))
fams = Family.from_ped(ped, order=vcf_order)
for fam_id in fams:
fams[fam_id] = (EvalFamily(fams[fam_id]),
[s._i for s in fams[fam_id].subjects])
def get_gene(variant):
for anno in annos:
consequences = variant.INFO[anno].split(",")
effs = (Effect.new(anno, c, annos[anno]) for c in consequences)
# limit to requested severity
if severity is not None:
effs = [e for e in effs if e.impact_severity in severity]
effs = sorted(effs, reverse=True)
for eff in effs:
if eff.gene:
return eff.gene
# TODO: more flexible groupby
for gene, variants in it.groupby(vcf, get_gene):
matching_fams = defaultdict(list)
saved_vars = []
uniq_fams = []
for i, variant in enumerate(variants):
saved_vars.append(variant)
for family_id, (fam, idxs) in fams.items():
fam.gt_types = variant.gt_types[idxs]
fam.gt_depths = variant.gt_depths[idxs]
fam.gt_quals = variant.gt_quals[idxs]
# this dispatches to fam.auto_rec/auto_dom/de_novo/, etc. by the string
# in inheritance model
res = getattr(fam, inheritance_model)(min_depth=min_depth,
min_gq=min_gq)
# matched the inheritance model.
if res: # can add custom logic here, e.g. and v.call_rate > 0.9:
matching_fams[i].append(family_id)
uniq_fams.append(family_id)
if 0 < len(set(uniq_fams)) >= min_kindreds:
if inheritance_model == 'comp_het':
# TODO: idxs = matching_fams.keys()
# run idxs[1:] vs idxs[:-1] for variants
pass
for i, family_ids in sorted(matching_fams.items()):
variant = saved_vars[i]
variant.INFO["inheritance"] = "%s:%s" % (gene, ",".join(
set(family_ids)))
out.write_record(variant)
def run(inheritance_model, ped, vcf, min_depth, min_gq, min_kindreds, severity):
from cyvcf2 import VCF, Writer
vcf = VCF(vcf, samples="-")
annos = {}
if "ANN" in vcf:
desc = vcf["ANN"]["Description"]
parts = [x.strip("\"'") for x in re.split("\s*\|\s*", desc.split(":", 1)[1].strip('" '))]
annos["ANN"] = desc
if "EFF" in vcf:
desc = vcf["EFF"]["Description"]
parts = [x.strip(" [])'(\"") for x in re.split("\||\(", desc.split(":", 1)[1].strip())]
annos["EFF"] = parts
if "CSQ" in vcf:
desc = vcf["CSQ"]["Description"]
parts = [x.strip(" [])'(\"") for x in re.split("\||\(", desc.split(":", 1)[1].strip())]
annos["CSQ"] = parts
vcf.update(id="inheritance", type="String", number="1", description="inheritance stuffs")
out = Writer("-", vcf)
vcf_order = dict((n, i) for i, n in (enumerate(vcf.samples)))
fams = Family.from_ped(ped, order=vcf_order)
for fam_id in fams:
fams[fam_id] = (EvalFamily(fams[fam_id]), [s._i for s in fams[fam_id].subjects])
def get_gene(variant):
for anno in annos:
consequences = variant.INFO[anno].split(",")
effs = (Effect.new(anno, c, annos[anno]) for c in consequences)
# limit to requested severity
if severity is not None:
effs = [e for e in effs if e.impact_severity in severity]
effs = sorted(effs, reverse=True)
for eff in effs:
if eff.gene:
return eff.gene
# TODO: more flexible groupby
for gene, variants in it.groupby(vcf, get_gene):
matching_fams = defaultdict(list)
saved_vars = []
uniq_fams = []
for i, variant in enumerate(variants):
saved_vars.append(variant)
for family_id, (fam, idxs) in fams.items():
fam.gt_types = variant.gt_types[idxs]
fam.gt_depths = variant.gt_depths[idxs]
fam.gt_quals = variant.gt_quals[idxs]
# this dispatches to fam.auto_rec/auto_dom/de_novo/, etc. by the string
# in inheritance model
res = getattr(fam, inheritance_model)(min_depth=min_depth, min_gq=min_gq)
# matched the inheritance model.
if res: # can add custom logic here, e.g. and v.call_rate > 0.9:
matching_fams[i].append(family_id)
uniq_fams.append(family_id)
if 0 < len(set(uniq_fams)) >= min_kindreds:
if inheritance_model == 'comp_het':
# TODO: idxs = matching_fams.keys()
# run idxs[1:] vs idxs[:-1] for variants
pass
for i, family_ids in sorted(matching_fams.items()):
variant = saved_vars[i]
variant.INFO["inheritance"] = "%s:%s" % (gene, ",".join(set(family_ids)))
out.write_record(variant)
