The pyp_classes Module

pyp_classes contains two base classes that are used by PyPedal, the Animal() class and the Pedigree() class. What most PyPedal routines recognize as a pedigree is actually just a Python list of Animal() objects. An instance of a Pedigree() object is a collection of METADATA about a list of Animals(). I know that this is confusing, and it is going to change by the time that PyPedal 2.0.0 final is released.

Module Contents

Animal(animalID, sireID, damID, gen='0', by=1900, sex='u', fa=0., name='u', alleles=['', ''], breed='u', age=-999, alive=-999) (class) [#]

The Animal() class is holds animals records read from a pedigree file.

For more information about this class, see The Animal Class.

Pedigree(myped, inputfile, name, pedcode='asd', reord=0, renum=0, debug=0) (class) [#]

The Pedigree() class stores metadata about pedigrees.

For more information about this class, see The Pedigree Class.

The Animal Class

Animal(animalID, sireID, damID, gen='0', by=1900, sex='u', fa=0., name='u', alleles=['', ''], breed='u', age=-999, alive=-999) (class) [#]

The Animal() class is holds animals records read from a pedigree file.

__init__(animalID, sireID, damID, gen='0', by=1900, sex='u', fa=0., name='u', alleles=['', ''], breed='u', age=-999, alive=-999) ⇒ object [#]

__init__() initializes an Animal() object.

self

Reference to the current Animal() object

animalID

Animal ID number

sireID

Sire ID number

damID

Dam ID number

gen

Generation to which the animal belongs

by

Birthyear of the animal

sex

Sex of the animal (m|f|u)

fa

Coefficient of inbreeding of the animal

name

Name of animal

alleles

A two-element array of strings, which represent allelotypes.

breed

Breed of animal

age

Age of animal

alive

Status of animal (alive or dead)

Returns:

An instance of an Animal() object populated with data

pad_id() ⇒ integer [#]

pad_id() takes an Animal ID, pads it to fifteen digits, and prepends the birthyear (or 1950 if the birth year is unknown). The order of elements is: birthyear, animalID, count of zeros, zeros.

self

Reference to the current Animal() object

Returns:

A padded ID number that is supposed to be unique across animals

printme() [#]

printme() prints a summary of the data stored in the Animal() object.

self

Reference to the current Animal() object

stringme() [#]

stringme() returns a summary of the data stored in the Animal() object as a string.

self

Reference to the current Animal() object

trap() [#]

trap() checks for common errors in Animal() objects

self

Reference to the current Animal() object

The Pedigree Class

Pedigree(myped, inputfile, name, pedcode='asd', reord=0, renum=0, debug=0) (class) [#]

The Pedigree() class stores metadata about pedigrees. Hopefully this will help improve performance in some procedures, as well as provide some useful summary data.

__init__(myped, inputfile, name, pedcode='asd', reord=0, renum=0, debug=0) ⇒ object [#]

__init__() initializes a Pedigree metata object.

self

Reference to the current Pedigree() object

myped

A PyPedal pedigree

inputfile

The name of the file from which the pedigree was loaded

name

The name assigned to the PyPedal pedigree

pedcode

The format code for the PyPedal pedigree

reord

Flag indicating whether or not the pedigree is reordered (0|1)

renum

Flag indicating whether or not the pedigree is renumbered (0|1)

Returns:

An instance of a Pedigree() object populated with data

fileme() [#]

fileme() writes the metada stored in the Pedigree() object to disc.

self

Reference to the current Pedigree() object

nud() ⇒ integer-and-list [#]

nud() returns the number of unique dams in the pedigree along with a list of the dams

self

Reference to the current Pedigree() object

Returns:

The number of unique dams in the pedigree and a list of those dams

nuf() ⇒ integer-and-list [#]

nuf() returns the number of unique founders in the pedigree along with a list of the founders

self

Reference to the current Pedigree() object

Returns:

The number of unique founders in the pedigree and a list of those founders

nug() ⇒ integer-and-list [#]

nug() returns the number of unique generations in the pedigree along with a list of the generations

self

Reference to the current Pedigree() object

Returns:

The number of unique generations in the pedigree and a list of those generations

nus() ⇒ integer-and-list [#]

nus() returns the number of unique sires in the pedigree along with a list of the sires

self

Reference to the current Pedigree() object

Returns:

The number of unique sires in the pedigree and a list of those sires

nuy() ⇒ integer-and-list [#]

nuy() returns the number of unique birthyears in the pedigree along with a list of the birthyears

self

Reference to the current Pedigree() object

Returns:

The number of unique birthyears in the pedigree and a list of those birthyears

printme() [#]

printme() prints a summary of the metadata stored in the Pedigree() object.

self

Reference to the current Pedigree() object

stringme() [#]

stringme() returns a summary of the metadata stored in the pedigree as a string.

self

Reference to the current Pedigree() object