Variant

Superclass for classes that create GA4GH VariantInterpretationObjects. Subclass HgvsVariant is used for small variants encoded using HGVS notation, e.g., NM_00123.5:c.543G>T. Subclass StructuralVariant is used for structural variants that are likely to completely disrupt a gene.

Source code in pyphetools/creation/variant.py

class Variant(metaclass=abc.ABCMeta):
    """
    Superclass for classes that create GA4GH VariantInterpretationObjects.
    Subclass HgvsVariant is used for small variants encoded using HGVS notation, e.g., NM_00123.5:c.543G>T.
    Subclass StructuralVariant is used for structural variants that are likely to completely disrupt a gene.

    """

    def __init__(self):
        self._genotype = None

    @abc.abstractmethod
    def to_ga4gh_variant_interpretation(self, acmg=None):
        """
        Embed the variant object into a GA4GH Genomic Interpretation object (abstract method)

        The argument acmg must be one of the strings 'benign', 'likely_benign', 'uncertain_significance',
            'likely_pathogenic', or 'pathogenic' (underscores are optional). If it is not provided or
            not one of these strings, the level will be set to not available

        :param acmg: ACMG pathogenicity level
        :type acmg: str
        """
        pass

    def set_heterozygous(self):
        """
        Assign heterozygous allele status to this variant

        """
        self._genotype = 'heterozygous'

    def set_homozygous(self):
        """
        Assign homozygous allele status to this variant

        """
        self._genotype = 'homozygous'

    def set_hemizygous(self):
        """
        Assign hemizygous allele status to this variant

        """
        self._genotype = 'hemizygous'

    def set_genotype(self, gt):
        """
        Assign an allele status to this variant

        :param gt: The genotype (allele status) of this variant

        """
        genotype = gt.lower()
        if genotype not in {'heterozygous', 'homozygous', 'hemizygous'}:
            raise ValueError(f"Unrecognized genotype {gt}")
        self._genotype = genotype

    @staticmethod
    def _get_genotype_term(genotype: str) -> typing.Optional[OntologyClass202]:
        if genotype is None:
            return None
        if genotype == "heterozygous":
            return OntologyClass202(id="GENO:0000135", label=genotype)
        elif genotype == "homozygous":
            return OntologyClass202(id="GENO:0000136", label=genotype)
        elif genotype == "hemizygous":
            return OntologyClass202(id="GENO:0000134", label=genotype)
        else:
            raise ValueError(f"Did not recognize genotype {genotype}")

    @staticmethod
    def _get_acmg_classification(acmg: str = None) -> ACMG202:
        """
        Get the Phenopacket Schema code for ACMG variant pathogenicity classification.
        """
        if acmg is None:
            return ACMG202.NOT_PROVIDED
        acmg = acmg.lower()
        acmg_d = {
            'benign': ACMG202.BENIGN,
            'likely benign': ACMG202.LIKELY_BENIGN,
            'likely_benign': ACMG202.LIKELY_BENIGN,
            'uncertain significance': ACMG202.UNCERTAIN_SIGNIFICANCE,
            'uncertain_significance': ACMG202.UNCERTAIN_SIGNIFICANCE,
            'likely pathogenic': ACMG202.LIKELY_PATHOGENIC,
            'likely_pathogenic': ACMG202.LIKELY_PATHOGENIC,
            'pathogenic': ACMG202.PATHOGENIC
        }
        if acmg in acmg_d:
            return acmg_d.get(acmg)
        else:
            print(f"Warning- did not recognize ACMG category {acmg}")
            return ACMG202.NOT_PROVIDED

set_genotype(gt)

Assign an allele status to this variant

Parameters:

Name	Type	Description	Default
gt		The genotype (allele status) of this variant	required

Source code in pyphetools/creation/variant.py

def set_genotype(self, gt):
    """
    Assign an allele status to this variant

    :param gt: The genotype (allele status) of this variant

    """
    genotype = gt.lower()
    if genotype not in {'heterozygous', 'homozygous', 'hemizygous'}:
        raise ValueError(f"Unrecognized genotype {gt}")
    self._genotype = genotype

set_hemizygous()

Assign hemizygous allele status to this variant

Source code in pyphetools/creation/variant.py

def set_hemizygous(self):
    """
    Assign hemizygous allele status to this variant

    """
    self._genotype = 'hemizygous'

set_heterozygous()

Assign heterozygous allele status to this variant

Source code in pyphetools/creation/variant.py

def set_heterozygous(self):
    """
    Assign heterozygous allele status to this variant

    """
    self._genotype = 'heterozygous'

set_homozygous()

Assign homozygous allele status to this variant

Source code in pyphetools/creation/variant.py

def set_homozygous(self):
    """
    Assign homozygous allele status to this variant

    """
    self._genotype = 'homozygous'

to_ga4gh_variant_interpretation(acmg=None) abstractmethod

Embed the variant object into a GA4GH Genomic Interpretation object (abstract method)

The argument acmg must be one of the strings 'benign', 'likely_benign', 'uncertain_significance', 'likely_pathogenic', or 'pathogenic' (underscores are optional). If it is not provided or not one of these strings, the level will be set to not available

Parameters:

Name	Type	Description	Default
acmg	str	ACMG pathogenicity level	None

Source code in pyphetools/creation/variant.py

@abc.abstractmethod
def to_ga4gh_variant_interpretation(self, acmg=None):
    """
    Embed the variant object into a GA4GH Genomic Interpretation object (abstract method)

    The argument acmg must be one of the strings 'benign', 'likely_benign', 'uncertain_significance',
        'likely_pathogenic', or 'pathogenic' (underscores are optional). If it is not provided or
        not one of these strings, the level will be set to not available

    :param acmg: ACMG pathogenicity level
    :type acmg: str
    """
    pass