Genotyping Protocols#

Class Family Overview#

The GenotypingProtocol family of classes is used to simulate the genotyping of individuals. GenotypeProtocol classes take a set of phased genomes (represented by a PhasedGenotypeMatrix) and return a (typically unphased) genotype matrix of the individuals in the input.

Summary of Genotyping Protocol Classes#

Genotyping protocols can be found in the pybrops.breed.prot.gt module. PyBrOpS currently only has a single implemented class in this family, the DenseUnphasedGenotyping class, which represents flawless, whole-genome unphased genotyping. The genotyping protocols module is deliberately left open for users to implement their own classes if so desired.

Summary of classes in the `pybrops.breed.prot.gt` module#
Class Name	Class Type	Class Description
`GenotypingProtocol`	Abstract	Interface for all genotyping protocol classes.
`DenseUnphasedGenotyping`	Concrete	Class representing whole-genome genotyping which produces a dense unphased genotype matrix.

Genotyping Protocol Properties#

Genotyping protocols do not have any required properties defined in their interface.

Loading Class Modules#

Genotyping protocols may be imported as illustrated below.

# import the GenotypingProtocol class (an abstract interface class)
from pybrops.breed.prot.gt.GenotypingProtocol import GenotypingProtocol

# import the DenseUnphasedGenotyping class (a concrete implemented class)
from pybrops.breed.prot.gt.DenseUnphasedGenotyping import DenseUnphasedGenotyping

Creating Genotyping Protocols#

Genotyping protocol class construction is entirely implementation dependent. Below is an example of how to construct a DenseUnphasedGenotyping object, which takes no arguments for its construction.

# object creation takes no arguments
gtprot = DenseUnphasedGenotyping()

Genotyping Individuals from their Genomes#

Individuals may be genotyped using the genotype method. This method takes a set of individual genomes (represented using a PhasedGenotypeMatrix) and returns a GenotypeMatrix representing genotyped individuals. A demonstration of how to use the genotype method is shown below.

#
# Construct random genomes
#

# shape parameters for random genomes
ntaxa = 100
nvrnt = 1000
ngroup = 20
nchrom = 10
nphase = 2

# create random genotypes
mat = numpy.random.randint(0, 2, size = (nphase,ntaxa,nvrnt)).astype("int8")

# create taxa names
taxa = numpy.array(["taxon"+str(i+1).zfill(3) for i in range(ntaxa)], dtype = object)

# create taxa groups
taxa_grp = numpy.random.randint(1, ngroup+1, ntaxa)
taxa_grp.sort()

# create marker variant chromsome assignments
vrnt_chrgrp = numpy.random.randint(1, nchrom+1, nvrnt)
vrnt_chrgrp.sort()

# create marker physical positions
vrnt_phypos = numpy.random.choice(1000000, size = nvrnt, replace = False)
vrnt_phypos.sort()

# create marker variant names
vrnt_name = numpy.array(["SNP"+str(i+1).zfill(4) for i in range(nvrnt)], dtype = object)

# create a phased genotype matrix from scratch using NumPy arrays
pgmat = DensePhasedGenotypeMatrix(
    mat = mat,
    taxa = taxa,
    taxa_grp = taxa_grp,
    vrnt_chrgrp = vrnt_chrgrp,
    vrnt_phypos = vrnt_phypos,
    vrnt_name = vrnt_name,
    ploidy = nphase
)

#
# Genotype individuals
#

# get unphased genotypes from phased genotypes
gmat = gtprot.genotype(pgmat=pgmat)

# check if output is unphased
out = isinstance(gmat, DenseGenotypeMatrix) and not isinstance(gmat, DensePhasedGenotypeMatrix)