P2Rank to PDBe-KB export

This repository holds scripts which are used to export P2Rank predictions to PDBe-KB.

PDBe-KB

More information about PDBe-KB can be found at:

• https://gitlab.ebi.ac.uk/pdbe-kb
• https://www.ebi.ac.uk/pdbe/pdbe-kb

You can register into the PDBe-KB mailing list for email notifications.

Quick start

Prerequisites

• Python 3
• Git

Installing

git clone https://github.com/skodapetr/p2rank-funpdbe.git
cd p2rank-funpdbe
git clone https://gitlabci.ebi.ac.uk/pdbe-kb/funpdbe/funpdbe-client.git
git clone https://gitlabci.ebi.ac.uk/pdbe-kb/funpdbe/funpdbe-schema.git
git clone https://gitlabci.ebi.ac.uk/pdbe-kb/funpdbe/funpdbe-validator.git

pip install jsonschema
pip install requests

Execution

• Copy input files into /data/p2rank-outputs.
• Setup python paths:
  • Windows: set PYTHONPATH=%cd%\funpdbe-validator\;%PYTHONPATH%
  • Others: export PYTHONPATH="$PWD/funpdbe-validator/:$PYTHONPATH"
• Run the conversion script:

python p2rank-to-funpdbe/p2rank-to-funpdbe.py
python p2rank-to-funpdbe/p2rank-to-funpdbe.py --threads 4