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.
- Animal(animalID, sireID, damID, gen='0', by='1950', sex='u', fa=0., name='none', alleles=['', '']) (class) [#]
-
The Animal() class is holds animals records read from a pedigree file.
- __init__(animalID, sireID, damID, gen='0', by='1950', sex='u', fa=0., name='none', alleles=['', '']) ⇒ 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
- 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,
zeros, count of zeros (DEPRECATED).
- self
-
Reference to the current Animal() object
- Returns:
-
A padded ID number that is supposed to be unique across animals
- pad_id_new() ⇒ integer [#]
-
pad_id_new() 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
- trap() [#]
-
trap() checks for common errors in Animal() objects
- self
-
Reference to the current Animal() object
- Pedigree(myped, inputfile, name, pedcode='asd', reord=0, renum=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) ⇒ 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