ThreeWayCross#

class pybrops.breed.prot.mate.ThreeWayCross.ThreeWayCross(progeny_counter=0, family_counter=0, rng=None, **kwargs)[source]#

Class implementing mating protocols for three-way crosses.

Constructor for the concrete class ThreeWayCross.

Parameters:

progeny_counter (Integral) – Progeny counter. This helps create progeny names.
family_counter (Integral) – Family counter. This helps label groups of progenies as originating from the same family.
rng (numpy.random.Generator, numpy.random.RandomState) – Random number source.
kwargs (dict) – Additional keyword arguments.

Methods

Mate individuals according to a 3-way mate selection scheme.

Attributes

`family_counter`	Description for property family_counter.
`nparent`	Number of parents the mating protocol requires.
`progeny_counter`	Description for property progeny_counter.
`rng`	Random number generator.

property family_counter: Integral#: Description for property family_counter.

mate(pgmat, xconfig, nmating, nprogeny, miscout=None, nself=0, **kwargs)[source]#

Mate individuals according to a 3-way mate selection scheme.

Parameters:

pgmat (DensePhasedGenotypeMatrix) – A GenotypeMatrix containing candidate breeding individuals.
xconfig (numpy.ndarray) –
A 1D array of indices of selected individuals of shape (k,).

Where:
- k is the number of selected individuals.
Indices are paired as follows:
- First index is the recurrent parent.
- Second index is the female parent.
- Third index is the male parent.
Example:
```
xconfig = [1,5,3,8,2,7]
recurrent = 1,8
female = 5,2
male = 3,7
```
nmating (numpy.ndarray) – Number of cross patterns to perform.
nprogeny (numpy.ndarray) – Number of doubled haploid progeny to generate per cross.
miscout (dict, None, default = None) – Pointer to a dictionary for miscellaneous user defined output. If dict, write to dict (may overwrite previously defined fields). If None, user defined output is not calculated or stored.
s (int, default = 0) – Number of selfing generations post-cross.
kwargs (dict) – Additional keyword arguments to be passed to constructor for the output DensePhasedGenotypeMatrix.

Returns:

out – A DensePhasedGenotypeMatrix of progeny.

Return type:

DensePhasedGenotypeMatrix

property nparent: Integral#: Number of parents the mating protocol requires.

property progeny_counter: Integral#: Description for property progeny_counter.