atbogetti/rhapsody

Python program, based on Prody, for pathogenicity prediction of human missense variants

Rhapsody

Python program, based on ProDy, for pathogenicity prediction of human missense variants.

The code of conduct is the same as for ProDy (https://github.com/prody/ProDy/blob/master/CODE_OF_CONDUCT.md).

Install latest published version using pip

Rhapsody is published on PyPI. To install Rhapsody, please use pip in the terminal:

$ pip install -U prody-rhapsody

It might be necessary to manually install the DSSP program, for instance by typing on Linux:

$ sudo apt install dssp

Install from source

Rhapsody is written in pure Python so no local compilation is needed.

To install all needed dependencies, we strongly suggest to use Conda and create a new environment with:

$ conda create -n rhapsody python=3 numpy scikit-learn requests pyparsing matplotlib biopython tqdm
$ conda activate rhapsody
$ pip install prody
$ conda install -c salilab dssp

After cloning/forking the Rhapsody repository, you can permanently add the repository path to the conda environment with:

$ conda develop path/to/local/repository

If not using Conda, you can manually install all dependencies and then add the repository location to the PYTHONPATH environmental variable. For example, on Linux simply add the following line to your ~/.bashrc:

export PYTHONPATH="path/to/local/repository/:$PYTHONPATH"

If you are running on Windows, please follow this tutorial.

Running initial setup

After installation, please run:

import rhapsody as rd
rd.initialSetup()