PedInterp 0.1.7

Image interpreter for clinical pedigrees for conversion to PED file formatting

Pedigree Interpreter Package

pedigree-interpreter is a python package used to interpretation images of clinical pedigrees into PED file formatting.

Prerequisites

This package depends on the Tesseract ORC Engine, which must be installed separately in addition to the Python dependencies listed in 'pyproject.toml'.

Installation instruction for Tesseract OCR engin are available in the official Teserract documentation:

tesseract Installation Guide

Installation

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

pip install pedigree-interpreter

Usage

This package has two main functions:

1. pedigree_processing(FamID, raw_image_dir, export, output_dir) - translates the clinical pedigree image (.png) with the name given as FamID as the file name into a Pandas dataframe with field corresponding to PED file formatting. If desired, the interpretted pedigree can automatically exported as a PED file to the desired output directory (output_dir)
2. PED_export(PED_df, output_dir) - exports a given PED file-formatted Pandas dataframe (PED_df, constructed via pedigree_processing) to a desired output directory. File will be named according to the Family ID listed in first individual entry in PED_df (i.e. output_dir/.ped)

License

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