def voight_painting(h):
"""Paint haplotypes, assigning a unique integer to each shared haplotype
prefix.
Parameters
----------
h : array_like, int, shape (n_variants, n_haplotypes)
Haplotype array.
Returns
-------
painting : ndarray, int, shape (n_variants, n_haplotypes)
Painting array.
indices : ndarray, int, shape (n_hapotypes,)
Haplotype indices after sorting by prefix.
"""
# check inputs
# N.B., ensure int8 so we can use cython optimisation
h = HaplotypeArray(np.asarray(h), copy=False)
if h.max() > 1:
raise NotImplementedError('only biallelic variants are supported')
if h.min() < 0:
raise NotImplementedError('missing calls are not supported')
# sort by prefix
indices = h.prefix_argsort()
h = np.take(h, indices, axis=1)
# paint
painting = paint_shared_prefixes(np.asarray(h))
return painting, indices
def ehh_decay(h, truncate=False):
"""Compute the decay of extended haplotype homozygosity (EHH)
moving away from the first variant.
Parameters
----------
h : array_like, int, shape (n_variants, n_haplotypes)
Haplotype array.
truncate : bool, optional
If True, the return array will exclude trailing zeros.
Returns
-------
ehh : ndarray, float, shape (n_variants, )
EHH at successive variants from the first variant.
"""
from allel.opt.stats import pairwise_shared_prefix_lengths_int8
# check inputs
# N.B., ensure int8 so we can use cython optimisation
h = HaplotypeArray(np.asarray(h, dtype="i1"), copy=False)
if h.max() > 1:
raise NotImplementedError("only biallelic variants are supported")
if h.min() < 0:
raise NotImplementedError("missing calls are not supported")
# initialise
n_variants = h.n_variants # number of rows, i.e., variants
n_haplotypes = h.n_haplotypes # number of columns, i.e., haplotypes
n_pairs = (n_haplotypes * (n_haplotypes - 1)) // 2
# compute the shared prefix length between all pairs of haplotypes
spl = pairwise_shared_prefix_lengths_int8(h)
# compute EHH by counting the number of shared prefixes extending beyond
# each variant
minlength = None if truncate else n_variants + 1
b = np.bincount(spl, minlength=minlength)
c = np.cumsum(b[::-1])[:-1]
ehh = (c / n_pairs)[::-1]
return ehh
def ehh_decay(h, truncate=False):
"""Compute the decay of extended haplotype homozygosity (EHH)
moving away from the first variant.
Parameters
----------
h : array_like, int, shape (n_variants, n_haplotypes)
Haplotype array.
truncate : bool, optional
If True, the return array will exclude trailing zeros.
Returns
-------
ehh : ndarray, float, shape (n_variants, )
EHH at successive variants from the first variant.
"""
from allel.opt.stats import pairwise_shared_prefix_lengths_int8
# check inputs
# N.B., ensure int8 so we can use cython optimisation
h = HaplotypeArray(np.asarray(h, dtype='i1'), copy=False)
if h.max() > 1:
raise NotImplementedError('only biallelic variants are supported')
if h.min() < 0:
raise NotImplementedError('missing calls are not supported')
# initialise
n_variants = h.n_variants # number of rows, i.e., variants
n_haplotypes = h.n_haplotypes # number of columns, i.e., haplotypes
n_pairs = (n_haplotypes * (n_haplotypes - 1)) // 2
# compute the shared prefix length between all pairs of haplotypes
spl = pairwise_shared_prefix_lengths_int8(h)
# compute EHH by counting the number of shared prefixes extending beyond
# each variant
minlength = None if truncate else n_variants + 1
b = np.bincount(spl, minlength=minlength)
c = np.cumsum(b[::-1])[:-1]
ehh = (c / n_pairs)[::-1]
return ehh
def voight_painting(h):
"""Paint haplotypes, assigning a unique integer to each shared haplotype
prefix.
Parameters
----------
h : array_like, int, shape (n_variants, n_haplotypes)
Haplotype array.
Returns
-------
painting : ndarray, int, shape (n_variants, n_haplotypes)
Painting array.
indices : ndarray, int, shape (n_hapotypes,)
Haplotype indices after sorting by prefix.
"""
from allel.opt.stats import paint_shared_prefixes_int8
# check inputs
# N.B., ensure int8 so we can use cython optimisation
h = HaplotypeArray(np.asarray(h, dtype="i1"), copy=False)
if h.max() > 1:
raise NotImplementedError("only biallelic variants are supported")
if h.min() < 0:
raise NotImplementedError("missing calls are not supported")
# sort by prefix
indices = h.prefix_argsort()
h = np.take(h, indices, axis=1)
# paint
painting = paint_shared_prefixes_int8(h)
return painting, indices