New: you can find the ECCB2022 poster here.

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

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 

Please check the tutorial here.

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

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

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