Metadata-Version: 2.1
Name: pypgatk
Version: 0.0.12
Summary: Python tools for proteogenomics
Home-page: http://github.com/bigbio/py-pgatk
Author: PgAtk Team
Author-email: ypriverol@gmail.com
License: LICENSE.txt
Description: # Python tools for ProteoGenomics Analysis Toolkit
        
        
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        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pypgatk/README.html)
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        ![PyPI - Downloads](https://img.shields.io/pypi/dm/pypgatk)
        
        **pypgatk** is a Python library part of the [ProteoGenomics Analysis Toolkit](https://pgatk.readthedocs.io/en/latest). It provides different bioinformatics tools for proteogenomics data analysis.
        
        # Requirements:
        
        This package requirements vary depending on the way that you want to install it (all three are independent, you don't need all these requirements):
        
        - pip: if installation goes through pip, you will require Python3 and pip3 installed.
        - Bioconda: if installation goes through Bioconda, you will require that [conda is installed and configured to use bioconda channels](https://bioconda.github.io/user/index.html).
        - Docker container: to use pypgatk from its docker container you will need [Docker](https://docs.docker.com/install/) installed.
        - Source code: to use and install from the source code directly, you will need to have git, Python3 and pip.
        
        # Installation
        
        ## pip
        
        You can install pypgatk with pip:
        
        ```
        pip install pypgatk
        ```
        
        ## Bioconda
        
        You can install pypgatk with bioconda (please setup conda and the bioconda channel if you haven't first, as explained [here](https://bioconda.github.io/user/index.html)):
        
        ```
        conda install pypgatk
        ```
        
        ## Available as a container
        
        You can use the pypgatk tool already setup on a Docker container. You need to choose from the available tags [here](https://quay.io/repository/biocontainers/pypgatk?tab=tags) and replace it in the call below where it says `<tag>`.
        
        ```
        docker pull quay.io/biocontainers/pypgatk:<tag>
        ```
        
        **NOTE**: Please note that Biocontainers containers do not have a latest tag, as such a docker pull/run without defining the tag will fail. For instance, a valid call would be (for version 0.0.2):
        
        ```
        docker run -it quay.io/biocontainers/pypgatk:0.0.2--py_0
        ```
        
        Inside the container, you can either use the Python interactive shell or the command line version (see below).
        
        
        ## Use latest source code
        
        Alternatively, for the latest version, clone this repo and go into its directory, then execute `pip3 install .` :
        
        ```
        git clone https://github.com/bigbio/py-pgatk
        cd py-pgatk
        # you might want to create a virtualenv for pypgatk before installing
        pip3 install .
        ```
        
        # Usage
        
        The pypgatk design combines multiple modules and tools into one framework. All the possible commands are accessible using the commandline tool `pypgatk_cli.py`.
        
        ```
        $: pypgatk_cli.py -h
        Usage: pypgatk_cli.py [OPTIONS] COMMAND [ARGS]...
        
          This is the main tool that give access to all commands and options
          provided by the pypgatk
        
        Options:
          -h, --help  Show this message and exit.
        
        Commands:
          cbioportal-downloader     Command to download the the cbioportal studies
          cbioportal-to-proteindb  Command to translate cbioportal mutation data into
                                   proteindb
          cosmic-downloader        Command to download the cosmic mutation database
          cosmic-to-proteindb      Command to translate Cosmic mutation data into
                                   proteindb
          dnaseq-to-proteindb      Generate peptides based on DNA sequences
          ensembl-downloader       Command to download the ensembl information
          generate-decoy           Create decoy protein sequences. Each protein is
                                   reversed and the cleavage sites switched with
                                   preceding amino acid. Peptides are checked for
                                   existence in target sequences if foundthe tool will
                                   attempt to shuffle them. James.Wright@sanger.ac.uk
                                   2015
          threeframe-translation   Command to perform 3frame translation
          vcf-to-proteindb         Generate peptides based on DNA variants from
                                   ENSEMBL VEP VCF files
        
        ```
        
        The library provides multiple commands to download, translate and generate protein sequence databases from reference and mutation genome databases.
        
        # Full Documentation
        
        [https://pgatk.readthedocs.io/en/latest/pypgatk.html](https://pgatk.readthedocs.io/en/latest/pypgatk.html)
        
        ## Cite as
        Yasset Perez-Riverol, & Husen M. Umer. (2021, February 3). bigbio/pypgatk: Pre-release v0.0.9 (Version v0.0.9). Zenodo. [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4499011.svg)](https://doi.org/10.5281/zenodo.4499011)
        
        
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