Dissecting the Promoter

Installation and Setup

Clone the project repository:

git clone https://github.com/AddisonHowe/promoter-dissection.git && cd promoter-dissection

Create a conda environment from the environment.yml file, and install all required dependencies.

conda env create -n <env-name> -f environment.yml
conda activate <env-name>

By default, installation excludes optional dependencies for enabling JAX acceleration, jupyter notebooks, and test development. These can be included by editing the environment.yml file to add the optional pip dependencies. Simply comment and uncomment the desired lines nested under pip. Alternatively, after activating the environment, rerun the pip installation with the desired options, for example:

conda activate <env-name>
# Install optional dependencies and specify editable install.
python -m pip install -e ".[jax,jupyter,dev]" 

Assuming all optional dependencies have been installed, check that all tests pass via:

conda activate <env-name>
pytest tests

Examples

Acknowledgments

This project was inspired by the work of the Rob Phillips Lab. In particular, the RegSeq project.

References

[1] William T Ireland, Suzannah M Beeler, Emanuel Flores-Bautista, Nicholas S McCarty, Tom Röschinger, Nathan M Belliveau, Michael J Sweredoski, Annie Moradian, Justin B Kinney, Rob Phillips (2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time eLife 9:e55308.