This chapter introduces the PyPedal Python extension and outlines the rest of the document.
PyPedal (Python Pedigree Analysis) is a tool for analyzing animal pedigree files. It calculates several quantitative measures of allelic and genoytpic diversity from pedigrees, including average coefficients of inbreeding and relationship, effective number of founders, and effective number of ancestors. Some qualitative checks are performed in order to catch some common mistakes, such as parents with more recent birthdates or ID numbers than their offspring.
Routines are also provided for the decomposition of and the direct formation of
with and without taking account of inbreeding. These are of academic interest rather than practical interest, but if a simple script is needed for the inversion of a reasonablysized pedigree PyPedal is quite adequate to the task.
PyPedal is a Python language module that may be called by other Python programs or used interactively from the command line in the Python interpreter. The Numerical Python module (http://www.pfdubois.com/numpy/) module is required by PyPedal, and is included with some Linux distributions.
This document is the ``official'' documentation for pypedal. It is both a tutorial and the most authoritative source of information about pypedal with the exception of the source code. The tutorial material will walk you through a set of manipulations of a simple pedigree. All users of pypedal are encouraged to follow the tutorial with a working pypedal installation, testing the examples. The best way to learn is by doing -- the aim of this tutorial is to guide you along this "doing."
This manual contains: