def test_highest():
effects = sorted(EFFECTS)
top = Effect.top_severity(effects)
assert isinstance(top, Effect)
assert top.impact_severity == "MED"
effects.append(effects[-1])
top = Effect.top_severity(effects)
assert isinstance(top, list)
assert top[0].impact_severity == "MED"
def test_highest():
effects = sorted(EFFECTS)
top = Effect.top_severity(effects)
assert top.impact_severity == "MED"
assert top.so == "missense_variant"
#assert top[0].
effects.append(effects[-1])
top = Effect.top_severity(effects)
assert isinstance(top, list)
assert top[0].impact_severity == "MED"
def test_highest():
effects = sorted(EFFECTS)
top = Effect.top_severity(effects)
assert isinstance(top, Effect)
assert top.impact_severity == "MED"
effects.append(effects[-1])
top = Effect.top_severity(effects)
assert isinstance(top, list)
assert top[0].impact_severity == "MED"
def test_highest():
effects = sorted(EFFECTS)
top = Effect.top_severity(effects)
assert top.impact_severity == "MED"
assert top.so == "missense_variant"
#assert top[0].
effects.append(effects[-1])
top = Effect.top_severity(effects)
assert isinstance(top, list)
assert top[0].impact_severity == "MED"
def getTopImpact(effects):
top_severe = Effect.top_severity(effects)
if type(top_severe) is list:
top_impact = top_severe[0].top_consequence
else:
top_impact = top_severe.top_consequence
return top_impact
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
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
VEP.keys = vcf_reader.infos['CSQ'].desc.split(" ")[-1].split("|")
novel = False
overlap_effects = defaultdict(int)
no_overlap_effects = defaultdict(int)
for record in vcf_reader:
maf = float(2 * record.num_hom_alt +
record.num_het) / (2 * record.num_called)
effects = []
for annot in record.INFO['CSQ']:
vep = VEP(annot)
effects.append(vep)
effects = sorted(effects) # last record - the most severe
top_severe = Effect.top_severity(effects)
if type(top_severe) is list:
top_impact = top_severe[0].impact_severity
else:
top_impact = top_severe.impact_severity
is_lof = isLoF(effects)
overlap_eur, overlap_afr, overlap_amr, overlap_eas, overlap_sas = overlapsExisting(
effects)
overlap_1kg = overlap_eur or overlap_afr or overlap_amr or overlap_eas or overlap_sas
if not overlap_1kg:
no_overlap_effects[top_impact] += 1
if is_lof: no_overlap_effects['LoF'] += 1
else:
overlap_effects[top_impact] += 1
if is_lof: overlap_effects['LoF'] += 1