Package: biobb-netprop
biobb_netpropIntroductionBioBB 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.Versionv1.0.0 2022.4InstallationIf you have no experience with anaconda, please first take a look to theNew with anaconda?section of theofficial documentation.Download repositoryAlthough the biobb_netprop repository is available at GitHub and thus you can clone it, we strongly recommend you todownload it compressedand start your new project from scratch.Create new conda environmentOnce you have the project unzipped in your computer, please follow the next steps to create a new conda environment:cd biobb_netpropconda env create -f conda_env/environment.ymlUpdate environment pathsEditconda_env/biobb_netprop.pthwith the paths to yourbiobb_netpropfolder. Example:/home/user_name/projects/biobb_netprop//home/user_name/projects/biobb_netprop/biobb_netprop/netptropCopy the editedconda_env/biobb_netprop.pthfile 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/anaconda3or/opt/conda.cp conda_env/biobb_netprop.pth /[anaconda-path]/envs/biobb_netprop/lib/python3.7/site-packagesActivate environmentThen, activate the recently createdbiobb_netpropconda environment:conda activate biobb_netpropCreate repositoryThis netprop includes some folders not standard for a biobb, such asbiobb_netprop/adapters/,biobb_netprop/notebooks/orconda_env/. For the sake of having a pure biobb structure, you should uncomment the three last lines of the.gitignorefile before creating a new git repository:biobb_netprop/adaptersbiobb_netprop/notebooksconda_envThen, inialitize repository:git initWorkFlow exampleIn this directory, there is also a implemented Python version of the Static WorkFlow, but for it to run, it ismandatoryto download and modify their paths in the YAML file, the DisGenet and the HIPPIE databases locally.
You can find themhere.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 configurationAdditionally, it's recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in theBinary path configurationsection of theofficial documentation.DocumentationClick here to find the API Documentation examplefor this BioBB andhere for Command Line documentation.And here you can findthe full documentationabout how to build a newBioExcel building blockfrom scratch.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728), Disc4All955735.(c) 2015-2020Barcelona Supercomputing Center(c) 2015-2020Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.