How to use the cyvcf2.Variant function in cyvcf2

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github kipoi / kipoiseq / tests / test_dataclasses.py View on Github external
v.alt = 'asd'

    # non-fixed arguments
    v.id = 'asd'
    v.qual = 10
    v.filter = 'asd'
    v.source = 2

    assert isinstance(Variant("chr1", '10', 'C', 'T').pos, int)

    # from cyvcf2
    vcf = cyvcf2.VCF('tests/data/test.vcf.gz')
    cv = list(vcf)[0]

    v2 = Variant.from_cyvcf(cv)
    assert isinstance(v2.source, cyvcf2.Variant)
github arq5x / gemini / gemini / annotations.py View on Github external
# Get variant ref, alt.
        var_ref, var_alt = _get_var_ref_and_alt(var)
        # no alternative alleles, return the original region_only hits
        if not var_alt or len(var_alt) == 0:
            return hits
        var_alt = set(var_alt)

        # Warn for multiple alleles.
        chrom, start, end = coords
        multiallele_warning(chrom, start, ','.join(var_alt), False)

        # Filter hits to those that match ref and alt.
        matched_hits = []
        for h in hits:
            if isinstance(h, (cyvcf2.Variant, pysam.VariantRecord)):
                start = h.start
            elif isinstance(h, basestring):
                start = int(h.split('\t', 2)[1]) - 1
            else:
                start = h.pos
            if start != coords[1]: continue

            anno_ref, anno_alt = _get_var_ref_and_alt(h)
            anno_alt = set(anno_alt)

            multiallele_warning(chrom, start, anno_alt, True)

            # Match via ref and set intersection of alternates.
            # the mappability uses "." as the alt for all rows. so
            if var_ref == anno_ref and (len(var_alt & anno_alt) >= 1 \
                    or anno_alt == set(".")):
github arq5x / gemini / gemini / annotations.py View on Github external
def _get_var_coords(var, naming):
    """Retrieve variant coordinates from multiple input objects.
    """
    if isinstance(var, cyvcf2.Variant):
      chrom, start, end = var.CHROM, var.start, var.end
    else:
        try:
            # todo: check isinstance resultproxy?
            chrom = var["chrom"]
            start = int(var["start"])
            end = int(var["end"])
        except TypeError:
            chrom = var.CHROM
            start = var.start
            end = var.end
    if naming == "ucsc":
        chrom = _get_chr_as_ucsc(chrom)
    elif naming == "grch37":
        chrom = _get_chr_as_grch37(chrom)
    return chrom, start, end

cyvcf2

fast vcf parsing with cython + htslib

MIT
Latest version published 6 months ago

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63 / 100
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