Metadata-Version: 1.2
Name: rpg
Version: 1.0.0
Summary: In silico protein digestion
Home-page: UNKNOWN
Author: Nicolas Maillet
Author-email: nicolas.maillet@pasteur.fr
Maintainer: Nicolas Maillet
Maintainer-email: nicolas.maillet@pasteur.fr
License: GPLv3
Description: RapidPeptidesGenerator (RPG)
        ============================
        
        Rapid Peptides Generator (RPG) is a software dedicated to predict proteases-induced cleavage sites on amino acid sequences.
        
        .. image:: https://badge.fury.io/py/rpg.svg
            :target: https://badge.fury.io/py/rpg
            :alt: Pypi repo
        
        .. image:: https://gitlab.pasteur.fr/nmaillet/rpg/badges/master/pipeline.svg
            :target: https://gitlab.pasteur.fr/nmaillet/rpg/commits/master
            :alt: Build Status
        
        .. image:: https://gitlab.pasteur.fr/nmaillet/rpg/badges/master/coverage.svg
            :target: https://gitlab.pasteur.fr/nmaillet/rpg/commits/master
            :alt: Coverage Report
        
        .. image:: https://readthedocs.org/projects/rapid-peptide-generator/badge/?version=latest
            :target: http://rapid-peptide-generator.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        :note: RPG is tested with Gitlab Ci for the following Python version: 3.4, 3.5 and 3.6
        :issues: Please use https://gitlab.pasteur.fr/nmaillet/rpg
        
        
        
        Overview
        ========
        
        Rapid Peptides Generator (RPG), is a standalone software dedicated to predict proteases-induced cleavage sites on sequences.
        
        RPG is a python tool taking a (multi-)fasta/fastq file of proteins as input and digest each of them. The digestion mode can be either 'concurrent', i.e. all enzymes are present at the same time during digestion, or 'sequential'. In sequential mode, each protein will be digested by each enzyme, one by one.
        
        The resulting peptides contain informations about positions of cleavage site, peptide sequences, length, mass as-well as an estimation of isoelectric point (pI) of each peptide. Shortly, the isoelectric point is the pH at which a peptide carries no net electrical charge and a good approximation can be computed on small molecules. Results are outputted in multi-fasta, CSV or TSV file.
        
        Currently, 42 enzymes and chemicals are included in RPG. The user can easily design new enzymes, using a simple yet powerful grammar. This grammar allows the user to design complex enzymes like trypsin or thrombin, including many exceptions and different cleavage sites. User-defined enzymes are then interpreted by RPG and included in the local installation of the software.
        
        RPG follows the standards for software development with continuous integration on Gitlab (https://gitlab.pasteur.fr/nmaillet/rpg) and automatic on-line documentation (https://rapid-peptide-generator.readthedocs.io).
        
        
        
        Installation
        ============
        
        In order to install RPG, you can use **pip**:
        
        .. code-block:: none
        
            pip3 install rpg
        
        This command installs RPG and its Python dependencies.
        
        
        Usage
        =====
        
        From the command line:
        
        .. code-block:: none
        
            rpg --help
        
Keywords: protein,peptide,enzyme,protease,digestion
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
