Exemplo n.º 1
0
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"
Exemplo n.º 2
0
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"
Exemplo n.º 3
0
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"
Exemplo n.º 4
0
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
Exemplo n.º 6
0
 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
Exemplo n.º 7
0
 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