PedGen 0.1.2

Realistic synthetic pedigree generation, visualization, and file export.

Pedigree Generation Package

PedGen is a python package that can be used to generate genetically realistic pedigrees. Generated pedigrees can be visualized as directed acyclic graphs and exported in PED file format.

Prerequisites

Some functionality included in PedGen relies on system-level dependencies, namely in instalation of Graphviz. Please ensure Graphviz is installed before using the pedigree visualization functionality:

Unix

sudo apt install graphviz libgraphviz-dev

macOS(Homebrew)

brew install graphviz

Installation

All required Python dependencies will be installed automatically with this package using pip.

pip install PedGen

Usage

The primary function included in this package, pedigree_generator, works to contruct a realistic pedigree based on mendelian inheritance patterns and alternate allele frequencies in accordance with Hardy-Weinberg equilibrium. The generated pedigree is represented as Pandas dataframe object followign PED file formatting. 'pedigree_generator(FamilyID, max_children, mode, generation_count, SpouseLikelihood = 0.6, AffectedSpouse = True, backpropLikelihood = 0.25, alt_freq = 0.1)' - returns a dataframe with familial relation, sex, and phenotype information for individuals in the generated pedigree. Parameters

FamilyID (string): the ID to be assigned to the family

License

[MIT] (https://choosealicense.com/licenses/mit/)