biobb-netprop 1.12.3
Biobb_NetProp is use case to build a prioritize PPI Network through Disc4All pre-process database REST API.
Requires Python: ==3.7.*
Keywords: Bioinformatics Workflows BioExcel Compatibility

[![](https://readthedocs.org/projects/biobb-template/badge/?version=latest)](https://biobb-template.readthedocs.io/en/latest/?badge=latest)

# biobb_netprop

## Introduction
BioBB formulated for the Disc4All EU project, containing functions for interrogating the DisGenet database, parsing the HIPPIE PPI database and using NetworkX to create basic nodes for a prioritized network based on the mentioned databases retrieval.
new Biobbs by the community.
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](http://biobb_netprop.readthedocs.io/en/latest/).

## Version
v1.0.0 2022.4

## Installation

If you have no experience with anaconda, please first take a look to the [New with anaconda?](https://biobb-documentation.readthedocs.io/en/latest/first_steps.html#new-with-anaconda) section of the [official documentation](https://biobb-documentation.readthedocs.io/en/latest/).

### 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:

```console
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:

```console
/home/user_name/projects/biobb_netprop/
/home/user_name/projects/biobb_netprop/biobb_netprop/netptrop
```

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*.

```console
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:

```console
conda activate biobb_netprop
```

### Create repository

This netprop 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:

```console
biobb_netprop/adapters
biobb_netprop/notebooks
conda_env
```
Then, inialitize repository:

```console
git init
```


### WorkFlow example

In this directory, there is also a implemented Python version of the Static WorkFlow, but for it to run, it is **mandatory** to download and modify their paths in the YAML file, the DisGenet and the HIPPIE databases locally. 
You can find them [here](https://github.com/mapoferri/datasets_netprop).
**Remember to unzip the files before using them, and remember also to modify the path of the directory/datasets in the YML file).**

### 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](https://biobb-documentation.readthedocs.io/en/latest/execution.html#binary-path-configuration) section of the [official documentation](https://biobb-documentation.readthedocs.io/en/latest/).

## Documentation

[Click here to find the API Documentation example](https://biobb-netprop.readthedocs.io/en/latest/netprop.html) for this BioBB and [here for Command Line documentation](http://biobb_netprop.readthedocs.io/en/latest/command_line.html).

And here you can find [the full documentation](https://biobb-documentation.readthedocs.io/en/latest/) about how to build a new **BioExcel building block** from scratch.

## Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)), Disc4All [955735](http://cordis.europa.eu/projects/955735).

* (c) 2015-2020 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2020 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)

Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

![alt-text-1](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")