PyPedal::pyp_classes::Animal Class Reference

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

List of all members.

Public Member Functions
def	__init__
	__init__() initializes an Animal() object.
def	printme
	printme() prints a summary of the data stored in the Animal() object.
def	stringme
	stringme() returns a summary of the data stored in the Animal() object as a string.
def	trap
	trap() checks for common errors in Animal() objects
def	pad_id
	pad_id() takes an Animal ID, pads it to fifteen digits, and prepends the birthyear (or 1950 if the birth year is unknown).
Public Attributes
	animalID
	renumberedID
	sireID
	damID
	gen
	igen
	sex
	by
	fa
	founder
	sons
	daus
	unks
	paddedID
	ancestor
	name
	breed
	alleles
	pedcomp
	age
	alive

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Detailed Description

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

A simple class to hold animals records read from a pedigree file.

Definition at line 34 of file pyp_classes.py.

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Member Function Documentation

def PyPedal::pyp_classes::Animal::__init__	(		self,
			animalID,
			sireID,
			damID,
			gen = '0',
			by = 1900,
			sex = 'u',
			fa = 0.,
			name = 'u',
			alleles = ['',
			breed = 'u',
			age = -999,
			alive = -999
	)

__init__() initializes an Animal() object.

Parameters:

	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 object

Initialize an animal record.

Definition at line 53 of file pyp_classes.py.

def PyPedal::pyp_classes::Animal::printme

(

self

)

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

Parameters:

self

Reference to the current Animal() object Print the contents of an animal record - used for debugging.

Definition at line 91 of file pyp_classes.py.

def PyPedal::pyp_classes::Animal::stringme

(

self

)

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

Parameters:

self

Reference to the current Animal() object Return the contents of an animal record as a string.

Definition at line 119 of file pyp_classes.py.

def PyPedal::pyp_classes::Animal::trap

(

self

)

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

Parameters:

self

Reference to the current Animal() object Trap common errors in pedigree file entries.

Definition at line 167 of file pyp_classes.py.

def PyPedal::pyp_classes::Animal::pad_id

(

self

)

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.

Parameters:

self

Reference to the current Animal() object

Returns:

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

Take an Animal ID, pad it to fifteen digits, and prepend the birthyear (or 1950 if the birth year is unknown)

Definition at line 185 of file pyp_classes.py.

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The documentation for this class was generated from the following file:

• PyPedal/pyp_classes.py