PhenotypingProtocol#

class pybrops.breed.prot.pt.PhenotypingProtocol.PhenotypingProtocol[source]#

Bases: Copyable, HDF5InputOutput

Abstract class defining interfaces for phenotyping protocols.

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

Genomic model metadata.
Phenotype simulation.
Manipulation and setting of environmental variance metadata.

Methods

`copy`	Make a shallow copy of the `Copyable` object.
`deepcopy`	Make a deep copy of the `Copyable` object.
`from_hdf5`	Read an object from an HDF5 file.
`phenotype`	Phenotype a set of genotypes using a genomic prediction model.
`set_H2`	Set the broad sense heritability for environments.
`set_h2`	Set the narrow sense heritability for environments.
`to_hdf5`	Write an object to an HDF5 file.

Attributes

`gpmod`	Genomic prediction model.
`var_err`	Pure error variance for each trait

abstract copy()#

Make a shallow copy of the Copyable object.

Returns:: out – A shallow copy of the Copyable object.
Return type:: Copyable

abstract deepcopy(memo)#

Make a deep copy of the Copyable object.

Parameters:: memo (dict, None) – An optional dictionary of memo metadata.
Returns:: out – A deep copy of the Copyable object.
Return type:: Copyable

abstract classmethod from_hdf5(filename, groupname)#

Read an object from an HDF5 file.

Parameters:

filename (str, Path, h5py.File) – If str, an HDF5 file name from which to read. If Path, an HDF5 file name from which to read. If h5py.File, an opened HDF5 file from which to read.
groupname (str, None) – If str, an HDF5 group name under which object data is stored. If None, object is read from base HDF5 group.

Returns:

out – An object read from an HDF5 file.

Return type:

HDF5InputOutput

abstract property gpmod: GenomicModel#: Genomic prediction model.

abstract phenotype(pgmat, miscout, **kwargs)[source]#

Phenotype a set of genotypes using a genomic prediction model.

Parameters:

pgmat (PhasedGenotypeMatrix) – Genomes of the individuals to phenotype.
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 pandas.DataFrame containing phenotypes for individuals.

Return type:

pandas.DataFrame

abstract set_H2(H2, pgmat, **kwargs)[source]#

Set the broad sense heritability for environments.

Parameters:

H2 (Real, numpy.ndarray) – Broad sense heritability.
pgmat (PhasedGenotypeMatrix) – Founder genotypes.
kwargs (dict) – Additional keyword arguments

Return type:

None

abstract set_h2(h2, pgmat, **kwargs)[source]#

Set the narrow sense heritability for environments.

Parameters:

h2 (Real, numpy.ndarray) – Narrow sense heritability.
pgmat (PhasedGenotypeMatrix) – Founder genotypes.
kwargs (dict) – Additional keyword arguments

Return type:

None

abstract to_hdf5(filename, groupname, overwrite)#

Write an object to an HDF5 file.

Parameters:

filename (str, Path, h5py.File) – If str, an HDF5 file name to which to write. If Path, an HDF5 file path to which to write. If h5py.File, an opened HDF5 file to which to write.
groupname (str, None) – If str, an HDF5 group name under which object data is stored. If None, object is written to the base HDF5 group.
overwrite (bool) – Whether to overwrite values in an HDF5 file if a field already exists.

Return type:

None

abstract property var_err: object#: Pure error variance for each trait