{
    "info": {
        "author": "Austin Crinklaw",
        "author_email": "acrinklaw@lji.org",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
            "Operating System :: Unix",
            "Programming Language :: Python :: 3"
        ],
        "description": "# HLAQuant\n### Author: Austin Crinklaw\n\n## What is it?\nHLAQuant is a pipeline that produces fast and accurate allele specific expression for HLA genes. This is done by quantifying on the peptide binding groove domain using Salmon with personalized sequences.\n\n## Requirements:\n- Linux OS\n- NCBI Blast+\n- Salmon -- please ensure Salmon is on your PATH!\n- Python 3+\n  - Python packages: Pandas, BioPython\n\n## How to use:\n\n### Installation:\nHLAQuant can be downloaded through PyPI using the following pip command.\n```shell\npip install hlaquant\n```\n\n### Input  \nHLAQuant takes two input files currently. \n- File one (-hla) consists of a sample_id and then a list of alleles corresponding to that sample's typing (tab separated)\n- File two (-fastq) consists of a sample_id and then a list of FASTQ files corresponding to that sample (paired-end or single-end)\nExamples of these inputs can be found under the 'test_data/' directory\n\n### Usage\n- A list of parameters and their descriptions can be found with the -h flag\n```shell\npython -m HLAQuant -h\n```\n\n### Output  \nThe output will match that of Salmons. It consists of a tab separated file containing the transcript ID (in this case, a specific HLA allele), as well as the number of reads. TPMs can be ignored as they will be inaccurate since we are only quantifying over a few sequences.\n\n## How does it work?\n- We first take the list of alleles and fetch the corresponding sequences from IMGT\n- Next we extract the sequences corresponding to their groove domains from these sequences\n- We build an index for quantification using these G-domain sequences\n- We then perform quantification using this index\n\nThe paper outlining this method in detail can be found [....somewhere when it is published]\n\n## References:\nThis pipeline would be unable to work without Salmon\n\nPatro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods.\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": "https://github.com/acrinklaw/hlaquant",
        "keywords": "",
        "license": "",
        "maintainer": "",
        "maintainer_email": "",
        "name": "hlaquant",
        "package_url": "https://pypi.org/project/hlaquant/",
        "platform": "",
        "project_url": "https://pypi.org/project/hlaquant/",
        "project_urls": {
            "Homepage": "https://github.com/acrinklaw/hlaquant"
        },
        "release_url": "https://pypi.org/project/hlaquant/0.0.2/",
        "requires_dist": [
            "pandas",
            "biopython"
        ],
        "requires_python": "",
        "summary": "HLAQuant - Get HLA allele specific expression",
        "version": "0.0.2"
    },
    "last_serial": 5626653,
    "releases": {
        "0.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "61682c85030c57efe8db8562827544ad",
                    "sha256": "957c1ed985e6a912bfd159b209c512dcc9ef0d53375de9cc0320d3aafbc5b2f1"
                },
                "downloads": -1,
                "filename": "hlaquant-0.0.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "61682c85030c57efe8db8562827544ad",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 1242181,
                "upload_time": "2019-08-02T22:00:58",
                "url": "https://files.pythonhosted.org/packages/23/60/8dc237a6a8916055953f8d5c9ab6719d83870e0e914506aa5a6661f10e50/hlaquant-0.0.1-py3-none-any.whl"
            }
        ],
        "0.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "d6427f4b17d532d48e3c59894842da8c",
                    "sha256": "ee4094cc4bda75b5248a1692b77c87903e66a859f5b83e2a17d69a0959b833e2"
                },
                "downloads": -1,
                "filename": "hlaquant-0.0.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "d6427f4b17d532d48e3c59894842da8c",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 1242154,
                "upload_time": "2019-08-02T22:24:58",
                "url": "https://files.pythonhosted.org/packages/e3/b4/bc03eec2e66bcb98ec1520319eb41d654e5d2afff70f7d7b8bafa52615ab/hlaquant-0.0.2-py3-none-any.whl"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "d6427f4b17d532d48e3c59894842da8c",
                "sha256": "ee4094cc4bda75b5248a1692b77c87903e66a859f5b83e2a17d69a0959b833e2"
            },
            "downloads": -1,
            "filename": "hlaquant-0.0.2-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "d6427f4b17d532d48e3c59894842da8c",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": null,
            "size": 1242154,
            "upload_time": "2019-08-02T22:24:58",
            "url": "https://files.pythonhosted.org/packages/e3/b4/bc03eec2e66bcb98ec1520319eb41d654e5d2afff70f7d7b8bafa52615ab/hlaquant-0.0.2-py3-none-any.whl"
        }
    ]
}