How to use the kipoiseq.dataclasses.Variant function in kipoiseq

def variant_queryable():
    vcf = MultiSampleVCF(vcf_file)
    return VariantIntervalQueryable(vcf, [
        (
            [
                Variant('chr1', 12, 'A', 'T'),
                Variant('chr1', 18, 'A', 'C', filter='q10'),
            ],
            Interval('chr1', 10, 20)
        ),
        (
            [
                Variant('chr2', 120, 'AT', 'AAAT'),
            ],
            Interval('chr2', 110, 200)
        )

def test_variant():
    v = Variant("chr1", 10, 'C', 'T')

    assert v.start == 9
    assert v.chrom == 'chr1'
    assert v.pos == 10
    assert v.ref == 'C'
    assert v.alt == 'T'
    assert isinstance(v.info, dict)
    assert len(v.info) == 0
    assert v.qual == 0
    assert v.filter == 'PASS'
    v.info['test'] = 10
    assert v.info['test'] == 10
    assert isinstance(str(v), str)

    # make sure the original got unchangd
    v2 = v.copy()

with pytest.raises(AttributeError):
        v.chrom = 'asd'
    with pytest.raises(AttributeError):
        v.pos = 10
    with pytest.raises(AttributeError):
        v.ref = 'asd'
    with pytest.raises(AttributeError):
        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)

from conftest import vcf_file, gtf_file, example_intervals_bed
import pyranges
from kipoiseq.dataclasses import Interval, Variant
from kipoiseq.extractors.vcf import MultiSampleVCF
from kipoiseq.extractors.vcf_matching import variants_to_pyranges, \
    pyranges_to_intervals,  intervals_to_pyranges, BaseVariantMatcher, \
    SingleVariantMatcher, MultiVariantsMatcher

intervals = [
    Interval('chr1', 1, 10, strand='+'),
    Interval('chr1', 23, 30, strand='-')
]

variants = [
    Variant('chr1', 4, 'T', 'C'),
    Variant('chr1', 5, 'A', 'GA'),
    Variant('chr1', 25, 'AACG', 'GA')
]

pr = pyranges.PyRanges(
    chromosomes='chr1',
    starts=[1, 23, 5],
    ends=[10, 30, 50],
    strands=['+', '-', '.']
)


def test_variants_to_pyranges():
    vcf = MultiSampleVCF(vcf_file)
    variants = list(vcf)
    df = variants_to_pyranges(variants).df
    assert df.shape[0] == len(variants)

def test_MultiSampleVCF__regions_from_variants(multi_sample_vcf):
    variants = [
        Variant('chr1', 4, 'T', 'C'),
        Variant('chr1', 25, 'AACG', 'GA'),
        Variant('chr1', 55525, 'AACG', 'GA'),
        Variant('chr10', 55525, 'AACG', 'GA')

    ]
    regions = multi_sample_vcf._regions_from_variants(variants)

    assert set(regions) == set([
        Interval('chr1', 3, 25),
        Interval('chr1', 55524, 55525),
        Interval('chr10', 55524, 55525)
    ])

def test_MultiSampleVCF_get_variant(multi_sample_vcf):

    variant = multi_sample_vcf.get_variant("chr1:4:T>C")
    assert variant.chrom == 'chr1'
    assert variant.pos == 4
    assert variant.ref == 'T'
    assert variant.alt == 'C'

    variant = multi_sample_vcf.get_variant(Variant('chr1', 4, 'T', 'C'))
    assert variant.chrom == 'chr1'
    assert variant.pos == 4
    assert variant.ref == 'T'
    assert variant.alt == 'C'

    with pytest.raises(KeyError):
        multi_sample_vcf.get_variant("chr1:4:A>C")

import pyranges
from kipoiseq.dataclasses import Interval, Variant
from kipoiseq.extractors.vcf import MultiSampleVCF
from kipoiseq.extractors.vcf_matching import variants_to_pyranges, \
    pyranges_to_intervals,  intervals_to_pyranges, BaseVariantMatcher, \
    SingleVariantMatcher, MultiVariantsMatcher

intervals = [
    Interval('chr1', 1, 10, strand='+'),
    Interval('chr1', 23, 30, strand='-')
]

variants = [
    Variant('chr1', 4, 'T', 'C'),
    Variant('chr1', 5, 'A', 'GA'),
    Variant('chr1', 25, 'AACG', 'GA')
]

pr = pyranges.PyRanges(
    chromosomes='chr1',
    starts=[1, 23, 5],
    ends=[10, 30, 50],
    strands=['+', '-', '.']
)


def test_variants_to_pyranges():
    vcf = MultiSampleVCF(vcf_file)
    variants = list(vcf)
    df = variants_to_pyranges(variants).df
    assert df.shape[0] == len(variants)

if number of variants in given limits.
    """

    def __init__(self, max_num=float('inf'), min_num=0):
        # TODO: sample speficity
        self.max_num = max_num
        self.min_num = min_num

    def __call__(self, variants, interval):
        if self.max_num >= len(variants) >= self.min_num:
            return [True] * len(variants)
        else:
            return [False] * len(variants)


_VariantIntervalType = List[Tuple[Iterable[Variant], Interval]]


class VariantIntervalQueryable:

    def __init__(self, vcf, variant_intervals: _VariantIntervalType,
                 progress=False):
        """
        Query object of variants.

        Args:
          vcf: cyvcf2.VCF objects.
          variants: iter of (variant, interval) tuples.
        """
        self.vcf = vcf
        self.variant_intervals = variant_intervals
        self.progress = progress