{
    "info": {
        "author": "PgAtk Team",
        "author_email": "ypriverol@gmail.com",
        "bugtrack_url": null,
        "classifiers": [],
        "description": "# Python tools for ProteoGenomics Analysis Toolkit\n\n\n[![Build Status](https://travis-ci.org/bigbio/py-pgatk.svg?branch=master)](https://travis-ci.org/bigbio/py-pgatk)\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pypgatk/README.html)\n\n\n**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.\n\n# Requirements:\n\nThis package requirements vary depending on the way that you want to install it (all three are independent, you don't need all these requirements):\n\n- pip: if installation goes through pip, you will require Python3 and pip3 installed.\n- 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).\n- Docker container: to use pypgatk from its docker container you will need [Docker](https://docs.docker.com/install/) installed.\n- Source code: to use and install from the source code directly, you will need to have git, Python3 and pip.\n\n# Installation\n\n## pip\n\nYou can install pypgatk with pip:\n\n```\npip install pypgatk\n```\n\n## Bioconda\n\nYou 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)):\n\n```\nconda install pypgatk\n```\n\n## Available as a container\n\nYou 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>`.\n\n```\ndocker pull quay.io/biocontainers/pypgatk:<tag>\n```\n\n**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):\n\n```\ndocker run -it quay.io/biocontainers/pypgatk:0.0.2--py_0\n```\n\nInside the container, you can either use the Python interactive shell or the command line version (see below).\n\n\n## Use latest source code\n\nAlternatively, for the latest version, clone this repo and go into its directory, then execute `pip3 install .` :\n\n```\ngit clone https://github.com/bigbio/py-pgatk\ncd py-pgatk\n# you might want to create a virtualenv for pypgatk before installing\npip3 install .\n```\n\n# Usage\n\nThe pypgatk design combines multiple modules and tools into one framework. All the possible commands are accessible using the commandline tool `pypgatk_cli.py`.\n\n```\n$: pypgatk_cli.py -h\nUsage: pypgatk_cli.py [OPTIONS] COMMAND [ARGS]...\n\n  This is the main tool that give access to all commands and options\n  provided by the pypgatk\n\nOptions:\n  -h, --help  Show this message and exit.\n\nCommands:\n  cbioportal-downloader     Command to download the the cbioportal studies\n  cbioportal-to-proteindb  Command to translate cbioportal mutation data into\n                           proteindb\n  cosmic-downloader        Command to download the cosmic mutation database\n  cosmic-to-proteindb      Command to translate Cosmic mutation data into\n                           proteindb\n  dnaseq-to-proteindb      Generate peptides based on DNA sequences\n  ensembl-downloader       Command to download the ensembl information\n  generate-decoy           Create decoy protein sequences. Each protein is\n                           reversed and the cleavage sites switched with\n                           preceding amino acid. Peptides are checked for\n                           existence in target sequences if foundthe tool will\n                           attempt to shuffle them. James.Wright@sanger.ac.uk\n                           2015\n  threeframe-translation   Command to perform 3frame translation\n  vcf-to-proteindb         Generate peptides based on DNA variants from\n                           ENSEMBL VEP VCF files\n\n```\n\nThe library provides multiple commands to download, translate and generate protein sequence databases from reference and mutation genome databases.\n\n### Please read full docs here: <https://pgatk.readthedocs.io/en/latest/pypgatk.html>\n\n\n",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "http://github.com/bigbio/py-pgatk",
        "keywords": "",
        "license": "Apache 2",
        "maintainer": "",
        "maintainer_email": "",
        "name": "pypgatk",
        "package_url": "https://pypi.org/project/pypgatk/",
        "platform": "",
        "project_url": "https://pypi.org/project/pypgatk/",
        "project_urls": {
            "Homepage": "http://github.com/bigbio/py-pgatk"
        },
        "release_url": "https://pypi.org/project/pypgatk/0.0.4/",
        "requires_dist": [
            "argcomplete (==1.9.5)",
            "argh (==0.26.2)",
            "asn1crypto (==0.24.0)",
            "astroid (==2.2.5)",
            "bcrypt (==3.1.6)",
            "biopython (==1.73)",
            "certifi (==2019.3.9)",
            "cffi (==1.12.3)",
            "chardet (==3.0.4)",
            "Click (==7.0)",
            "cryptography (==2.6.1)",
            "gffutils (==0.9)",
            "idna (==2.8)",
            "isort (==4.3.18)",
            "lazy-object-proxy (==1.4.0)",
            "mccabe (==0.6.1)",
            "numpy (==1.16.3)",
            "paramiko (==2.4.2)",
            "pyasn1 (==0.4.5)",
            "pycparser (==2.19)",
            "pyfaidx (==0.5.5.2)",
            "pylint (==2.3.1)",
            "PyNaCl (==1.3.0)",
            "pysftp (==0.2.9)",
            "PyVCF (==0.6.8)",
            "PyYAML (==5.1)",
            "requests (==2.21.0)",
            "simplejson (==3.16.0)",
            "six (==1.12.0)",
            "typed-ast (==1.3.5)",
            "urllib3 (==1.24.2)",
            "wrapt (==1.11.1)"
        ],
        "requires_python": "",
        "summary": "Python tools for proteogenomics",
        "version": "0.0.4"
    },
    "last_serial": 5668597,
    "releases": {
        "0.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c1d48d09d17a7581bd3d9f803e79536d",
                    "sha256": "d703a4d27fa395b9142f8b8e70d395f7f03f42f033562fe6451f775e77a80791"
                },
                "downloads": -1,
                "filename": "pypgatk-0.0.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "c1d48d09d17a7581bd3d9f803e79536d",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 54459,
                "upload_time": "2019-08-12T14:24:53",
                "url": "https://files.pythonhosted.org/packages/c6/15/026a0b310b971e87594c14a87184577c699482c817dfccb2cc6b0c9e8817/pypgatk-0.0.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "afa40ab52547d58de501cf8dc0a41891",
                    "sha256": "814fc9cbe31477f074701cd1f335da36cfb977b1585fd0a2ecde3f35fa703df1"
                },
                "downloads": -1,
                "filename": "pypgatk-0.0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "afa40ab52547d58de501cf8dc0a41891",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 39391,
                "upload_time": "2019-08-12T14:24:55",
                "url": "https://files.pythonhosted.org/packages/0c/57/4ce561c44428bd227de2bae1c1f806b08f341466cebad87e7624f16670cf/pypgatk-0.0.2.tar.gz"
            }
        ],
        "0.0.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "2c2e872fc9831dfd3c0febaa23dd5b62",
                    "sha256": "bcee0006509bbb2473ec3e0ee09d0528db400ce6398d416447e8d49eccb45c41"
                },
                "downloads": -1,
                "filename": "pypgatk-0.0.3-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "2c2e872fc9831dfd3c0febaa23dd5b62",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 54772,
                "upload_time": "2019-08-12T16:13:53",
                "url": "https://files.pythonhosted.org/packages/e9/92/c1cd7bcec90d93de7f98cf8d18c0933c6554efd130cdd12e0e00dfcc1bf1/pypgatk-0.0.3-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "cc0ac283440a368c18dd748104bcfa80",
                    "sha256": "f6724e8f32dc6e09623aa7496487f854ca65af9f0836d22cce7f7ea7f5dd3379"
                },
                "downloads": -1,
                "filename": "pypgatk-0.0.3.tar.gz",
                "has_sig": false,
                "md5_digest": "cc0ac283440a368c18dd748104bcfa80",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 39770,
                "upload_time": "2019-08-12T16:13:54",
                "url": "https://files.pythonhosted.org/packages/af/ae/3594fcc5186789d2e7fd77ffe7132ecd8fe81c3f7c4083f444360f9ebed6/pypgatk-0.0.3.tar.gz"
            }
        ],
        "0.0.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "cb4df5959d9ed25ca70ca22a86ac9039",
                    "sha256": "884ee9e9a2c7bf8f6b48bfdbae2052c355b2403b8493cd50e46e378081dc22a3"
                },
                "downloads": -1,
                "filename": "pypgatk-0.0.4-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "cb4df5959d9ed25ca70ca22a86ac9039",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 54770,
                "upload_time": "2019-08-12T20:24:54",
                "url": "https://files.pythonhosted.org/packages/2c/6a/e00731e487cc4ca9e46ef4d625248d11dd7b7cb706788c4903af0dd7287d/pypgatk-0.0.4-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "d5163324e7cc54d0868f01ed0507a111",
                    "sha256": "c249729dcd9c344f88469826a7d023cd4ada3236172832fa90a950208b8576da"
                },
                "downloads": -1,
                "filename": "pypgatk-0.0.4.tar.gz",
                "has_sig": false,
                "md5_digest": "d5163324e7cc54d0868f01ed0507a111",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 39889,
                "upload_time": "2019-08-12T20:24:56",
                "url": "https://files.pythonhosted.org/packages/ce/d1/67b3f09ea3c94157dcfa5821338ce733a37b8e1644961f674c4562d43b7f/pypgatk-0.0.4.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "cb4df5959d9ed25ca70ca22a86ac9039",
                "sha256": "884ee9e9a2c7bf8f6b48bfdbae2052c355b2403b8493cd50e46e378081dc22a3"
            },
            "downloads": -1,
            "filename": "pypgatk-0.0.4-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "cb4df5959d9ed25ca70ca22a86ac9039",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": null,
            "size": 54770,
            "upload_time": "2019-08-12T20:24:54",
            "url": "https://files.pythonhosted.org/packages/2c/6a/e00731e487cc4ca9e46ef4d625248d11dd7b7cb706788c4903af0dd7287d/pypgatk-0.0.4-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "d5163324e7cc54d0868f01ed0507a111",
                "sha256": "c249729dcd9c344f88469826a7d023cd4ada3236172832fa90a950208b8576da"
            },
            "downloads": -1,
            "filename": "pypgatk-0.0.4.tar.gz",
            "has_sig": false,
            "md5_digest": "d5163324e7cc54d0868f01ed0507a111",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 39889,
            "upload_time": "2019-08-12T20:24:56",
            "url": "https://files.pythonhosted.org/packages/ce/d1/67b3f09ea3c94157dcfa5821338ce733a37b8e1644961f674c4562d43b7f/pypgatk-0.0.4.tar.gz"
        }
    ]
}