https://readthedocs.org/projects/biobb-netprop/badge/?version=latest

biobb_netprop

Introduction

Biobb_NetProp is a complete code containing singular function for the DisGenet retrieval, the HIPPIE PPi database and the NetworkX for producing a prioritize PPi network, based on the gene/variants/disease attributes coming out of DisGenet. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v1.0.0 2022.4

Installation

If you have no experience with anaconda, please first take a look to the New with anaconda? section of the official documentation.

Download repository

Although the biobb_netprop repository is available at GitHub and thus you can clone it, we strongly recommend you to download it compressed and start your new project from scratch.

Create new conda environment

Once you have the project unzipped in your computer, please follow the next steps to create a new conda environment:

cd biobb_netprop
conda env create -f conda_env/environment.yml

Update environment paths

Edit conda_env/biobb_netprop.pth with the paths to your biobb_netprop folder. Example:

/home/user_name/projects/biobb_netprop/
/home/user_name/projects/biobb_netprop/biobb_netprop/biobb_netprop

Copy the edited conda_env/biobb_netprop.pth file to the site-packages folder of your environment. This folder is in /[anaconda-path]/envs/biobb_netprop/lib/python3.7/site-packages, where /[anaconda-path] is usually /anaconda3 or /opt/conda.

cp conda_env/biobb_netprop.pth /[anaconda-path]/envs/biobb_netprop/lib/python3.7/site-packages

Activate environment

Then, activate the recently created biobb_netprop conda environment:

conda activate biobb_netprop

Create repository

This directory includes some folders not standard for a biobb, such as biobb_netprop/adapters/, biobb_netprop/notebooks/ or conda_env/. For the sake of having a pure biobb structure, you should uncomment the three last lines of the .gitignore file before creating a new git repository:

biobb_netprop/adapters
biobb_netprop/notebooks
conda_env

Then, inialitize repository:

git init

Binary paths configuration

Additionally, it’s recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in the Binary path configuration section of the official documentation.

Documentation

Click here to find the API Documentation example for this netprop and here for Command Line documentation.

And here you can find the full documentation about how to build a new BioExcel building block from scratch.