HugoGuillen / genehtracker

Gene ID History Tracker

genehtracker - Gene ID History Tracker

New: you can find the ECCB2022 poster here.

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Objectives

The main objectives of this project are:

1. Generate putative mappings for deprecated/retired ENSEMBL IDs
2. Retrieve latest coordinates for a list of ENSEMBL IDs
3. Find the complete (GENCODE) annotation history of a gene ID
4. Find the complete (GENCODE) annotation history of a gene symbol
5. Build locally an index of GENCODE annotations

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Installation

The project is being developed in Python 3. A conda environment could be setup as:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

conda install mamba -n base -c conda-forge

mamba create -n genehtracker python=3 nomkl pandas matplotlib networkx bedtools graphviz pygraphviz python-graphviz pydot ucsc-liftover seaborn 

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Tutorial

Please check the tutorial here.

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TODO:

Functionality

• Add functions for finding gene ids
• Allow figure size parameter
• Save figures
• Add helper classes
• Command line diagrams
• Command line tables

Documentation

• Tutorial for object oriented
• Tutorial for command line
• Poster
• Add new dependencies (python-Levenshtein, seaborn, python-graphviz, pydot, ucsc-liftover)
• Export environment to yml

QoL

• Log messages while creating index
• Prefilter first and last genes to speed up intersection and index creation