/genehtracker

Gene ID History Tracker

Primary LanguageJupyter NotebookMIT LicenseMIT

genehtracker - Gene ID History Tracker

gru

New: you can find the ECCB2022 poster here.

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

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

Tutorial

Please check the tutorial here.

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