Biobb_NetProp is use case to build a prioritize PPI Network through Disc4All pre-process database REST API.
Project description
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.
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/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.
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 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:
biobb_netprop/adapters
biobb_netprop/notebooks
conda_env
Then, inialitize repository:
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. 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 section of the official documentation.
Documentation
Click here to find the API Documentation example for this BioBB 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.
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728), Disc4All 955735.
- (c) 2015-2020 Barcelona Supercomputing Center
- (c) 2015-2020 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
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