4.2.1 The Anatomy of a Pedigree File

Obviously you need a pedigree file in order to work with PyPedal. There are a couple of things that you need to know about pedigree files and at least one thing that is helpful to know. Pedigree files must contain a format code, and the format code must precede the first animal record. A complete list of pedigree codes appears in section 3.2. Each animal record must appear on a separate line in the pedigree file. An animal record consists of at least an animal ID, a sire ID, and a dam ID; the IDs are separated by a delimiter, usually a comma or a space. More information may be required on a linde depending on the pedigree format used. Missing parents should be coded as `0'. Parents do not need to have their own entry in the pedigree if THEIR parents are unknown; the preprocess() procedure is clever enough to add the needed records automatically. Comment lines, which begin with `#', may appear anywhere in the file; they are ignored by the preprocessor.
# Great tit pedigree from Hartl and Clark (1989), figure 5, p. 242.
# Used in PyPedal tutorial.
% asd
1 0 0
2 0 0
3 0 0
4 1 2
5 1 2
6 3 4
7 3 4
8 5 0
9 0 6
10 7 0
11 8 0
12 9 11
13 12 7
14 10 11
15 13 14
This pedigree contains fifteen animals, including three founders (animals with neither parent known), in the familiar 'animal sire dam' format.