{
    "info": {
        "author": "Xiao Li",
        "author_email": "xiaoli@broadinstitute.org",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.4",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# vbtools: a variant benchmark tool to compare VCFs with a consensus set\n## Install\nBefore installation, make sure [conda](https://docs.conda.io/en/latest/miniconda.html) is under your `PATH`. Conda installation [here](https://docs.conda.io/en/latest/miniconda.html).\n\n```sh\n# clone this repo\ngit clone git@github.com:broadinstitute/vbtools.git\n\n# setup conda environment\ncd vbtools\n\nconda env create -f env.yml # this will take a few minutes\nconda list  # verify new environment was installed correctly\n\n# activate environment\nconda activate vbtools\n\n# deactivate the environment when done\nconda deactivate\n\n# completely remove the virtual environment\nconda remove -name vbtools --all\n```\n\n## Usage\nYou can use following command to benchmark a VCF against a reference/consensus VCF.\n```sh\nvcfbench.py -v <input.vcf> -b <reference.vcf>\n```\n`--prefix` is an option to define prefix to the output files.\n\nCurrently, only haploid VCF is supported in the analysis. Diploid VCF will be standardized into haploid before comparison. Input VCF should follow [VCF spec v4.2](https://samtools.github.io/hts-specs/VCFv4.2.pdf).\n\nFollowing pre-processing steps are performed on the input VCF before the analysis:\n1) remove unused alleles\n2) remove monomorphic sites\n3) remove sites with heterozygous genotypes\n4) remove non-SNP sites\n5) remove sites with asterisk marks\n6) change diploid to haploid VCF\n\nThe script will output:\n1) Site level comparison:\n    - a tsv file including number of unique and shared sites.\n2) Sample level comparision:\n    - The sample level comparison functionality will be added to the script soon.\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/broadinstitute/vbtools",
        "keywords": "bioinformatics",
        "license": "MIT",
        "maintainer": "",
        "maintainer_email": "",
        "name": "vbtools",
        "package_url": "https://pypi.org/project/vbtools/",
        "platform": "",
        "project_url": "https://pypi.org/project/vbtools/",
        "project_urls": {
            "Bug tracker": "https://github.com/broadinstitute/vbtools/issues",
            "Documentation": "https://github.com/broadinstitute/vbtools/README.md",
            "Homepage": "https://github.com/broadinstitute/vbtools"
        },
        "release_url": "https://pypi.org/project/vbtools/0.1.0/",
        "requires_dist": [
            "vbtools (>=0.1.0)",
            "numpy (>=1.15.4pandas>=0.23.4)",
            "matplotlib (>=3.0.2)",
            "seaborn (>=0.9.0)"
        ],
        "requires_python": "",
        "summary": "A pipeline for analyzing fungal genomic data",
        "version": "0.1.0"
    },
    "last_serial": 5447148,
    "releases": {
        "0.1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "da219a04d9ff72e526a21f1004624d31",
                    "sha256": "105e1c88db2dbab344a1fed078e7f715eda9ae9a26b54a48dfbf88284dfab69b"
                },
                "downloads": -1,
                "filename": "vbtools-0.1.0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "da219a04d9ff72e526a21f1004624d31",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 7796,
                "upload_time": "2019-06-25T16:45:59",
                "url": "https://files.pythonhosted.org/packages/d3/b2/34d2693223978c037b912111c0a670835c12b99e4877831b1f13bacbbec6/vbtools-0.1.0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "80fb9e1892dd10196d62dc28285c088c",
                    "sha256": "6efcd364cf07c0e6d5ce9979c03d71b3a1f8254fdda38dcff5ce327a67b9dc76"
                },
                "downloads": -1,
                "filename": "vbtools-0.1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "80fb9e1892dd10196d62dc28285c088c",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5103,
                "upload_time": "2019-06-25T16:46:00",
                "url": "https://files.pythonhosted.org/packages/91/63/60807d208790a81613d1cb12e995822e9866b9574de346bb171809405d75/vbtools-0.1.0.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "da219a04d9ff72e526a21f1004624d31",
                "sha256": "105e1c88db2dbab344a1fed078e7f715eda9ae9a26b54a48dfbf88284dfab69b"
            },
            "downloads": -1,
            "filename": "vbtools-0.1.0-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "da219a04d9ff72e526a21f1004624d31",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": null,
            "size": 7796,
            "upload_time": "2019-06-25T16:45:59",
            "url": "https://files.pythonhosted.org/packages/d3/b2/34d2693223978c037b912111c0a670835c12b99e4877831b1f13bacbbec6/vbtools-0.1.0-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "80fb9e1892dd10196d62dc28285c088c",
                "sha256": "6efcd364cf07c0e6d5ce9979c03d71b3a1f8254fdda38dcff5ce327a67b9dc76"
            },
            "downloads": -1,
            "filename": "vbtools-0.1.0.tar.gz",
            "has_sig": false,
            "md5_digest": "80fb9e1892dd10196d62dc28285c088c",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 5103,
            "upload_time": "2019-06-25T16:46:00",
            "url": "https://files.pythonhosted.org/packages/91/63/60807d208790a81613d1cb12e995822e9866b9574de346bb171809405d75/vbtools-0.1.0.tar.gz"
        }
    ]
}