haplobin#

pybrops.core.util.haplo.haplobin(nhaploblk_chrom, genpos, chrgrp_stix, chrgrp_spix)[source]#

Given the number of haplotype blocks to give to each chromosome across the genome, assign bins for each marker

Parameters:

nhaploblk_chrom (numpy.ndarray) –
Array of shape (c,) containing the total number of haplotype blocks to assign to each chromosome across the genome.

Where:
- c is the number of chromosomes.
genpos (numpy.ndarray) –
Array of shape (p,) containing genetic positions of markers across the genome.

Where:
- p is the number of markers.
Input contraints:
- Must be sorted in ascending order.
- Must be grouped based on chromosome. The chromosome boundary start and stop indices must be provided in chrgrp_stix and chrgrp_spix, respectively.
chrgrp_stix (numpy.ndarray) –
Chromosome boundary start indices array of shape (c,).

Where:
- c is the number of chromosomes.
chrgrp_spix (numpy.ndarray) –
Chromosome boundary stop indices array of shape (c,).

Where:
- c is the number of chromosomes.

Returns:

out – Array of shape (p,) containing haplotype bin assignments for each marker across the genome. Bins are assigned starting at 0 and strictly increase as the index in the array increases due to constraints placed on genpos.

Where:

p is the number of markers.

Example output:

[0,0,0,0,0,1,1,1,1,1,1,1,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3]

Return type:

numpy.ndarray