Welcome to prunito’s documentation!

A package providing tools for accessing and working with protein sequences and associated data. The focus is on data from the UniProt Knowledgebase. This is reflected in the package name which is an anagram of UniProt. In addition to UniProt data, a few tools for accessing and/or working data from EuropePMC, InterPro and ENA are provided.

Installing prunito

Prunito is packaged as a wheel and can be installed using pip. This will also install all the dependencies. Python >=3.6 is required. As usual, it probably best to install prunito and its dependencies into a dedicated virtual environment.

  1. Create a virtual environment

    Using conda from the Anaconda Python distribution :

    • Create a new environment (env) called prunito which runs Python 3.6 and has pip installed:

      conda create -n prunito python=3.6 pip

    • Activate the env:

      conda activate prunito

    Using venv in a regular Python installation. Python is usually available out of the box on Linux:

    • Ensure that the version of Python used is 3.6 or higher:

      python --version

    • Create a new environment (env) called prunito. ensurepip will bootstrap pip into the env:

      pyvenv /path/to/new/virtual/environment/prunito

  2. Install prunito with its dependencies:

    pip install prunito-<version-py3-none-any>.whl

Dependencies

All of the following packages have to be installed some of which come with their own dependencies but those should be taken care of by running the usual pip command:

UniProtKB flat file parser

UniProt: parsers for flat file and uniRule format

UniProt: REST API

Indices and tables