diachrscripts

This is a collection of Python modules, scripts and Jupyter notebooks that can be used to investigate Diachromatic interactions in terms of the four counts for the different orientations of mapped paired-end reads.

Setup

First you need to clone this repository with:

$ git clone https://github.com/TheJacksonLaboratory/diachrscripts.git

Check which Python version you are using:

python --version

For convenience, you could do something like this: alias python=python3.9. We tested Python versions 3.7, 3.8, 3.9 and 3.10 on macOS. For Python version 3.11 we get an error when installing the pysam package.

Then change into the cloned directory, create a virtual environment and activate it:

$ cd diachrscripts
$ python -m venv dscripts
$ source dscripts/bin/activate

We use the Python package pybedtools, which requires BedTools to be installed and available through the $PATH variable. To install BedTools follow these instructions.

Install all required packages into this environment:

(dscripts)$ pip install -r requirements.txt

This may take a few minutes to complete. Depending on your Python installation, you may get an error message saying that Python.h is missing. In this case, install python-devel and execute the last command again.

Jupyter notebooks

To make the environment available in Jupyter notebooks create a Jupyter kernel.

(dscripts)$ pip install ipykernel
(dscripts)$ python -m ipykernel install --user --name=dscripts

When using Jupyter notebooks select the kernel dscripts.

Most of the analysis in diachrscripts is done in Jupyter notebooks. To get started with the analyses, change into the directory jupyter_notebooks and launch the notebook server.

(dscripts)$ cd jupyter_notebooks
(dscripts)$ jupyter-notebook

Depending on the configurations, a browser window will then open automatically, showing the contents of the directory from which the notebook server was started. If this is not the case, copy the URL that was output to the terminal and paste it into your browser's address bar. In the browser, select the notebook Get_started.ipynb.

Documentation

Change into the docs directory and generate the ReadTheDocs documentation as follows:

(dscripts)$ cd docs
(dscripts)$ make html

You should now find documentation here: diachrscripts/docs/_build/html/index.html

Testing

Run all tests as follows:

(dscripts)$ python -m unittest discover tests/

To deactivate the environment use deactivate.