3.5 Pedigree Files

Pedigree files consist of plain-text files (also known as ASCII or flatfiles) whose rows contain records on individual animals and whose columns contain different variables. The columns are delimited (separated from one another) by some character such as a space or a tab (\t). Pedigree files may also contain comments (notes) about the pedigree that are ignored by PyPedal; comments always begin with an octothorpe (#). For example, the following pedigree contains records for 13 animals, and each record contains three variables (animal ID, sire ID, and dam ID):
# This pedigree is taken from Boichard et al. (1997).
# Each records contains an animal ID, a sire ID, and
# a dam ID.
1 0 0
2 0 0
3 0 0
4 0 0
5 2 3
6 0 0
7 5 6
8 0 0
9 1 2
10 4 5
11 7 8
12 7 8
13 7 8
When this pedigree is processed by PyPedal the comments are ignored. If you need to change the default column delimiter , which is a space (' '), set the sepchar option to the desired value. For example, if your columns are tab-delimited you would set the option as:
options['sepchar'] = '\t'
Options are discussed at length in section 3.4. PyPedal also provides tools for pedigree simulation, which are discussed in section 3.8. More details about pedigree input may be found in Chapter 4.



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