GenotypingProtocol

class pybrops.breed.prot.gt.GenotypingProtocol.GenotypingProtocol

Bases: object

Abstract class defining genotyping protocols.

The purpose of this abstract class is to define functionality for:

1. Genotyping of individuals (converting a genome matrix to genotype matrix).

Methods

genotype

Genotype a genome.

abstract genotype(pgmat, miscout, **kwargs)

Genotype a genome.

Parameters:

• pgmat (PhasedGenotypeMatrix) – A phased genotype matrix representing the whole simulated genome.

• miscout (dict, 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.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A GenotypeMatrix of genotyped individuals.

Return type:

GenotypeMatrix