def take(self, indices, axis=0, out=None, mode='raise', **kwargs):
return take_genotypes(self, indices, axis=axis, wrap_axes={0, 1}, cls=type(self),
take=_chunked.take, out=out, mode=mode, **kwargs)
def subset(self, sel0=None, sel1=None, **kwargs):
return subset_genotype_array(self, sel0, sel1, cls=type(self),
subset=_chunked.subset, **kwargs)
def concatenate(self, others, axis=0, **kwargs):
return concatenate_genotypes(self, others, axis=axis, wrap_axes={0, 1},
cls=type(self), concatenate=_chunked.concatenate,
**kwargs)
# copy docstrings
copy_method_doc(GenotypeChunkedArray.fill_masked, GenotypeArray.fill_masked)
copy_method_doc(GenotypeChunkedArray.subset, GenotypeArray.subset)
copy_method_doc(GenotypeChunkedArray.is_called, GenotypeArray.is_called)
copy_method_doc(GenotypeChunkedArray.is_missing, GenotypeArray.is_missing)
copy_method_doc(GenotypeChunkedArray.is_hom, GenotypeArray.is_hom)
copy_method_doc(GenotypeChunkedArray.is_hom_ref, GenotypeArray.is_hom_ref)
copy_method_doc(GenotypeChunkedArray.is_hom_alt, GenotypeArray.is_hom_alt)
copy_method_doc(GenotypeChunkedArray.is_het, GenotypeArray.is_het)
copy_method_doc(GenotypeChunkedArray.is_call, GenotypeArray.is_call)
copy_method_doc(GenotypeChunkedArray.to_haplotypes, GenotypeArray.to_haplotypes)
copy_method_doc(GenotypeChunkedArray.to_n_ref, GenotypeArray.to_n_ref)
copy_method_doc(GenotypeChunkedArray.to_n_alt, GenotypeArray.to_n_alt)
copy_method_doc(GenotypeChunkedArray.to_allele_counts, GenotypeArray.to_allele_counts)
copy_method_doc(GenotypeChunkedArray.to_packed, GenotypeArray.to_packed)
# TODO
# copy_method_doc(GenotypeChunkedArray.from_packed, GenotypeArray.from_packed)
out = self.apply_method('to_gt',
kwargs=dict(phased=phased,
max_allele=max_allele),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def map_alleles(self, mapping, **storage_kwargs):
def f(block, bmapping):
return block.map_alleles(bmapping, copy=False)
domain = (self, mapping)
out = _chunked.apply(domain, f, **storage_kwargs)
return GenotypeChunkedArray(out)
# copy docstrings
copy_method_doc(GenotypeChunkedArray.fill_masked,
_ndarray.GenotypeArray.fill_masked)
copy_method_doc(GenotypeChunkedArray.subset,
_ndarray.GenotypeArray.subset)
copy_method_doc(GenotypeChunkedArray.is_called,
_ndarray.GenotypeArray.is_called)
copy_method_doc(GenotypeChunkedArray.is_missing,
_ndarray.GenotypeArray.is_missing)
copy_method_doc(GenotypeChunkedArray.is_hom,
_ndarray.GenotypeArray.is_hom)
copy_method_doc(GenotypeChunkedArray.is_hom_ref,
_ndarray.GenotypeArray.is_hom_ref)
copy_method_doc(GenotypeChunkedArray.is_hom_alt,
_ndarray.GenotypeArray.is_hom_alt)
copy_method_doc(GenotypeChunkedArray.is_het,
_ndarray.GenotypeArray.is_het)
copy_method_doc(GenotypeChunkedArray.is_call,
kwargs=dict(phased=phased,
max_allele=max_allele),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def map_alleles(self, mapping, **storage_kwargs):
def f(block, bmapping):
return block.map_alleles(bmapping, copy=False)
domain = (self, mapping)
out = _chunked.apply(domain, f, **storage_kwargs)
return GenotypeChunkedArray(out)
# copy docstrings
copy_method_doc(GenotypeChunkedArray.fill_masked,
_ndarray.GenotypeArray.fill_masked)
copy_method_doc(GenotypeChunkedArray.subset, _ndarray.GenotypeArray.subset)
copy_method_doc(GenotypeChunkedArray.is_called,
_ndarray.GenotypeArray.is_called)
copy_method_doc(GenotypeChunkedArray.is_missing,
_ndarray.GenotypeArray.is_missing)
copy_method_doc(GenotypeChunkedArray.is_hom, _ndarray.GenotypeArray.is_hom)
copy_method_doc(GenotypeChunkedArray.is_hom_ref,
_ndarray.GenotypeArray.is_hom_ref)
copy_method_doc(GenotypeChunkedArray.is_hom_alt,
_ndarray.GenotypeArray.is_hom_alt)
copy_method_doc(GenotypeChunkedArray.is_het, _ndarray.GenotypeArray.is_het)
copy_method_doc(GenotypeChunkedArray.is_call, _ndarray.GenotypeArray.is_call)
copy_method_doc(GenotypeChunkedArray.to_haplotypes,
_ndarray.GenotypeArray.to_haplotypes)
copy_method_doc(GenotypeChunkedArray.to_n_ref, _ndarray.GenotypeArray.to_n_ref)
return self._method_drop_axis2('to_gt', phased=phased,
max_allele=max_allele)
def to_haplotypes(self):
out = self.reshape(self.shape[0], -1)
return view_subclass(out, HaplotypeDaskArray)
def to_n_ref(self, fill=0, dtype='i1'):
return self._method_drop_axis2('to_n_ref', fill=fill, dtype=dtype)
def to_n_alt(self, fill=0, dtype='i1'):
return self._method_drop_axis2('to_n_alt', fill=fill, dtype=dtype)
# copy docstrings
copy_method_doc(GenotypeDaskArray.fill_masked,
_ndarray.GenotypeArray.fill_masked)
copy_method_doc(GenotypeDaskArray.subset,
_ndarray.GenotypeArray.subset)
copy_method_doc(GenotypeDaskArray.is_called,
_ndarray.GenotypeArray.is_called)
copy_method_doc(GenotypeDaskArray.is_missing,
_ndarray.GenotypeArray.is_missing)
copy_method_doc(GenotypeDaskArray.is_hom,
_ndarray.GenotypeArray.is_hom)
copy_method_doc(GenotypeDaskArray.is_hom_ref,
_ndarray.GenotypeArray.is_hom_ref)
copy_method_doc(GenotypeDaskArray.is_hom_alt,
_ndarray.GenotypeArray.is_hom_alt)
copy_method_doc(GenotypeDaskArray.is_het,
_ndarray.GenotypeArray.is_het)
copy_method_doc(GenotypeDaskArray.is_call,
