A Manual for use of PyPedal
A software package for pedigree analysis
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Contents
List of Tables
List of Figures
1. Introduction
1.1 Features
1.2 Where to get information and code
1.3 Acknowledgments
1.4 Disclaimer
2. Installing PyPedal
2.1 Overview of installation
2.2 Testing the Python installation
2.3 Installing PyPedal
2.3.1 Installing on Unix, Linux, and Mac OSX
2.3.2 Installing on Windows
2.4 Testing the PyPedal Installation
3. High-Level Overview
3.1 Interacting with PyPedal
3.2 The PyPedal Object Model
3.3 Program Structure
3.4 Options
3.4.1 Configuration Files
3.5 Pedigree Files
3.5.1 Pedigree Format Codes
3.6 Renumbering a Pedigree
3.6.1 Animal Identification
3.7 Logging
3.8 Simulating Pedigrees
4. Input and Output
4.1 Overview
4.2 Input
4.2.1 Graph Objects
4.2.2 GEDCOM Files
4.2.3 GENES Files
4.2.4 Text Files
4.2.5 Text Streams
4.3 Output
4.3.1 GEDCOM Files
4.3.2 GENES Files
4.3.3 Graph Objects
4.3.4 Text Files
4.3.5 Text Streams
4.4 Databases
4.4.1 Input from Databases
4.4.2 Output to Databases
5. Working with Pedigrees
5.1 Overview
5.2 Inbreeding and Relationships
5.3 Matings
5.4 Relatives
5.5 Decomposition and Direct Inverses of Numerator Relationship Matrices
6. Using PyPedal Objects
6.1 Animal Objects
6.1.1 The NewAnimal Class
6.1.2 The LightAnimal Class
6.1.3 The SimAnimal Class
6.2 The NewPedigree Class
6.3 The PedigreeMetadata Class
6.4 The NewAMatrix Class
7. Methodology
7.1 Reordering and Renumbering
7.2 Animal Identification and Cross-References
7.3 Measures of Genetic Variation
7.4 Computational Details
7.4.1 Inbreeding and Related Measures
7.4.2 Ancestral Inbreeding
7.4.3 Partial Inbreeding
7.4.4 Generation Coefficients
7.4.5 Effective Founder Number
7.4.6 Founder Genome Equivalents
7.4.7 Effective Ancestor Number
7.4.8 Pedigree Completeness
8. HOWTOs
8.1 Basic Tasks
8.1.1 How do I load a pedigree from a file?
8.1.2 How do I load multiple pedigrees in one program?
8.1.3 How do I renumber a pedigree?
8.1.4 How do I turn off output messages?
8.1.5 How do I load a pedigree whose columns are comma-delimited?
8.1.6 How do I load a pedigree whose columns are tab-delimited?
8.2 Calculating Measures of Genetic Variation
8.2.1 How do I calculate coefficients of inbreeding?
8.3 Databases and Report Generation
8.3.1 How do I load a pedigree into a database?
8.3.2 How do I update a pedigree in the database?
8.4 Pedigrees as Graphs
8.4.1 How do I convert a pedigree to a graph?
8.4.2 How do I convert a graph to a pedigree?
8.4.3 How do I load a pedigree from a file containing a graph stored as an adjacency list?
8.4.4 How do I save a graph as an adjacency list?
8.5 Miscellaneous
8.5.1 How do I export a numerator relationship matrix so that I can read it into Octave?
8.5.2 How else can I export a NRM to a file?
8.5.3 How do I load a pedigree from a GEDCOM file?
8.5.4 How do I save a pedigree to a GEDCOM file?
8.5.5 How do I load a pedigree from a string?
8.6 Contribute a HOWTO
9. Graphics
9.1 PyPedal Graphics
9.1.1 Drawing Pedigrees
9.1.2 Drawing Line Graphs
9.1.3 Visualizing Numerator Relationship Matrices
10. Report Generation
10.1 Overview
10.1.1 Three Generation Pedigrees
10.2 Creating a Custom Internal Report
10.3 Creating a Custom Printed Report
11. Implementing New Features
11.1 Overview
11.1.1 Defining the Problem
11.2 Module Template
11.3 Solving the Problem
11.4 Contributing Code to PyPedal
12. Glossary
A. Example Programs
B. GEDCOM File Handling
C. GENES File Handling
Bibliography
Index
A Manual for use of PyPedal
A software package for pedigree analysis
Previous:
License
Up:
A Manual for use
Next:
List of Tables
Release 2.0.3, documentation updated on November 29, 2005
Revised May 15, 2012.
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