conservation-scores-dataset 0.0.1

Python package providing retrieval for conservation scores.

Pipeline to automatically retrieve and preprocess conservation scores

Installing the package

As for any python package, simply run:

pip install conservation_scores_dataset

Usage examples

The following two usage examples will show both how to run the pipeline and how to retrieve the already pre-computed values stored within this GitHub repository.

Running the pipeline to retrieve the data

If you want to run the pipeline yourself, after taking note that some preprocessed data are already available within this repository, consider that the downloaded file will require a total size of ADDSIZE.

After having installed the package, just run the following to retrieve all data relative to the FANTOM5 and ROADMAP datasets for enhancers and promoters:

from conservation_scores_dataset import retrieve_all
retrieve_all()

It will display some loading bars showing you what the pipeline is doing at a given time, such as the following ones:

Based on the main loop provided in the retrieve all file, other similar automati retrieval pipelines for other BED files can be trivially built.