ChromFormer

This project aims to predict the shape of the Chromatin using Hi-C interaction matrices as input. It implements the following paper.

Environment

First, install python 3.8. If python 3.8 is already installed, you can use

python3 -m venv chromenv
source venv/bin/activate
pip install --upgrade pip setuptools wheel

To create your virtual environment. If python 3.8 is not installed the following can be done:

Mac

brew install pyenv
pyenv install 3.8 
pyenv local ["full version of python that got install"]
brew install pyenv-virtualenv 
eval "$(pyenv init -)"         
eval "$(pyenv virtualenv-init -)"
pyenv virtualenv ["full version of python that got install"] chromenv
pyenv local chromenv 

Windows

git clone https://github.com/pyenv-win/pyenv-win.git "$HOME\.pyenv"

[System.Environment]::SetEnvironmentVariable('PYENV',$env:USERPROFILE + "\.pyenv\pyenv-win\","User")

[System.Environment]::SetEnvironmentVariable('PYENV_ROOT',$env:USERPROFILE + "\.pyenv\pyenv-win\","User")

[System.Environment]::SetEnvironmentVariable('PYENV_HOME',$env:USERPROFILE + "\.pyenv\pyenv-win\","User")

[System.Environment]::SetEnvironmentVariable('path', $env:USERPROFILE + "\.pyenv\pyenv-win\bin;" + $env:USERPROFILE + "\.pyenv\pyenv-win\shims;" + [System.Environment]::GetEnvironmentVariable('path', "User"),"User")

pyenv install ["compatible 3.8 windows version"]

pyenv local ["full version of python that got install"]

python -m pip install -user virtualenv

python -m venv chromenv

pyenv local chromenv

.\chromenv\Scripts\activate

Package installation

Then you will need to install the ChromFormer package

pip install "git+ssh://git@github.com:AI4SCR/ChromFormer.git"

Suggested setup for development

# pip install pyg-lib torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.13.0+cpu.html
pip install -r requirements.txt
# pip install -e ".[dev]"
pre-commit install

Package Documentation

Find Documentation for Code here

Code organisation

The Following is the organisation of the repository:

ChromFormer is the package that contains the Uniform_Cluster_Walk.py data_generation file, Data_Tools that consist of optimal transport, plots and calculations needed for the Model and Data generation process.

bench consists of all experiments attempted such as data generation, model training and comparision with previous works. To use jupyter notebooks in the bench you will need to create a .env file at the root of the repository with variable DATA_DIR="your path to the data file". Directions on further organisation of the bench and which files to run are given in the README of the bench folder. A demo of an end to end example is given in the demo folder inside the bench.

data folder contains the generated synthetic and imported data