{
    "info": {
        "author": "lyam.baudry@pasteur.fr",
        "author_email": "",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: MacOS",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX",
            "Operating System :: Unix",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Visualization"
        ],
        "description": "# metaTOR\n\n[![PyPI version](https://badge.fury.io/py/metator.svg)](https://badge.fury.io/py/metator)\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/metator.svg)\n[![Build Status](https://travis-ci.com/koszullab/metaTOR.svg)](https://travis-ci.com/koszullab/metaTOR)\n[![Docker Automated build](https://img.shields.io/docker/build/koszullab/metator.svg)](https://hub.docker.com/r/koszullab/metator/)\n[![Read the docs](https://readthedocs.org/projects/metator/badge)](https://metator.readthedocs.io)\n[![License: GPLv3](https://img.shields.io/badge/License-GPL%203-0298c3.svg)](https://opensource.org/licenses/GPL-3.0)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)\n\nMetagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamline the processing and binning of metagenomic 3C datasets.\n\n## Installation\n\n```sh\n   pip3 install metator\n```\n\nor, to use the latest version:\n\n```sh\n   pip3 install -e git+https://github.com/koszullab/metator.git@master#egg=metator\n```\n\nPython 3.4 or later is required. A [standalone version](https://github.com/koszullab/metaTOR/tree/python3-standalone) (no installation, just download/unzip/run) is also available, as well as a [Python 2 version](https://github.com/koszullab/metaTOR/tree/python2), but keep in mind that development will focus on the current branch.\n\n## Usage\n\n    metator {align|partition|annotation|binning} [parameters]\n\nA metaTOR command takes the form ```metator action --param1 arg1 --param2\narg2 #etc.```\n\nThere are four actions/steps in the metaTOR pipeline, which must be run in the following order:\n\n* ```align``` : map paired-end reads on a preliminary assembly, then generate a network from\n detected contacts between DNA chunks.\n\n* ```partition``` : perform the Louvain community detection algorithm many times to isolate\n     chunks that consistently cluster together for binning purposes.\n\n* ```annotation``` : run standard annotation software on the assembly (namely gene prediction\n      and database comparison) to match with the bins.\n\n* ```binning``` : match annotations to bins, extract bin genomes and subnetworks, build bin-local\n   and global contact maps.\n\nAfter the last step is completed there should be a set of bins, their relative enrichments in various gene categories, and the contact map of each bin.\n\nThere are a number of other, optional, miscellaneous actions:\n\n* ```pipeline``` : check the environment is right, then run all four of the above actions sequentially.\n    This can take a while.\n\n* ```dependencies``` : download third party dependencies that are not available in most package managers.\n\n* ```deploy``` : set up the environment and all dependencies for Ubuntu 14.04 and higher (run as root).\n\n* ```version``` : display current version number.\n\n* ```help``` : display this help message.\n\nPlease refer to the [tutorial](https://github.com/koszullab/metaTOR/blob/master/doc/TUTORIAL.md) in order to quickly get the pipeline up and running on example data (or your own), and the [metaTOR manual](https://github.com/koszullab/metaTOR/blob/master/metator_manual.pdf) for detailed explanations on the parameters.\n\n## Requirements\n\n* Python 3 with ```numpy```, ```scipy```, ```matplotlib```, ```biopython``` and ```pysam``` libraries.\n* [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)\n* [samtools](http://www.htslib.org/)\n* [hmmer](http://hmmer.org/) and some HMM databases (such as [these](http://dl.pasteur.fr/fop/LItxiFe9/hmm_databases.tgz))\n* [prodigal](https://github.com/hyattpd/Prodigal)\n* [louvain](https://sourceforge.net/projects/louvain/) (original\n    implementation)\n\nRequirements can usually be installed with an OS's package manager. The requirements that cannot (namely ```prodigal```, ```louvain``` and HMM databases) can be fetched with the following (The package may need to be run as a root depending on where the package is installed):\n\n```sh\n    metator dependencies\n```\n\n## Containers\n\nA dockerfile is also available if that is of interest. You may fetch the image by running the following:\n\n```sh\n    docker pull koszullab/metator\n```\n\nAdditionally, a [Singularity](https://www.sylabs.io/) file is also available, courtesy of [avilab](https://github.com/avilab/metator). You may fetch the container this way:\n\n```sh\n    singularity pull shub://kosullab/metator\n```\n\n## References\n\n* [Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381813/), Martial Marbouty, Axel Cournac, Jean-Fran\u00e7ois Flot, Herv\u00e9 Marie-Nelly, Julien Mozziconacci, and Romain Koszul, eLife, 2014\n* [Meta3C analysis of a mouse gut microbiome](https://www.biorxiv.org/content/early/2015/12/17/034793), Martial Marbouty, Lyam Baudry, Axel Cournac, Romain Koszul, 2015\n* [Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315449/), Martial Marbouty, Lyam Baudry, Axel Cournac, and Romain Koszul, Science Advances, 2017\n\n## Contact\n\n### Authors\n\n* lyam.baudry@pasteur.fr\n* thfoutel@pasteur.fr\n* martial.marbouty@pasteur.fr\n* romain.koszul@pasteur.fr\n\n### Research lab\n\n[Spatial Regulation of Genomes](https://research.pasteur.fr/en/team/spatial-regulation-of-genomes/) (Institut Pasteur, Paris)\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/koszullab/metator",
        "keywords": "",
        "license": "GPLv3",
        "maintainer": "",
        "maintainer_email": "",
        "name": "metator",
        "package_url": "https://pypi.org/project/metator/",
        "platform": "",
        "project_url": "https://pypi.org/project/metator/",
        "project_urls": {
            "Homepage": "https://github.com/koszullab/metator"
        },
        "release_url": "https://pypi.org/project/metator/0.1.7/",
        "requires_dist": [
            "numpy",
            "scipy",
            "matplotlib",
            "biopython",
            "pysam",
            "seaborn",
            "setuptools"
        ],
        "requires_python": ">=3.4",
        "summary": "A pipeline for binning metagenomic datasets from 3C data.",
        "version": "0.1.7"
    },
    "last_serial": 4735416,
    "releases": {
        "0.1.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "30b3df907332580b5c35eafb15651ce0",
                    "sha256": "2cb13d77b606687db9a678d7454ad17d82c894a3db63f91cdce0e0c6777dfc28"
                },
                "downloads": -1,
                "filename": "metator-0.1.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "30b3df907332580b5c35eafb15651ce0",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3002743,
                "upload_time": "2018-11-11T18:10:38",
                "url": "https://files.pythonhosted.org/packages/fc/d8/25ae1823266a8c59aafd961ba3a3c3422d895290003502197c148c84557d/metator-0.1.1-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "419d284d34b0a7bf56824dcb4f0ac50d",
                    "sha256": "7811fe55c75cc21c2e1f54a1f0d8e95eb89a5f91ef0a836db1ca23ee97f66480"
                },
                "downloads": -1,
                "filename": "metator-0.1.1.tar.gz",
                "has_sig": false,
                "md5_digest": "419d284d34b0a7bf56824dcb4f0ac50d",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 2968436,
                "upload_time": "2018-11-11T18:10:42",
                "url": "https://files.pythonhosted.org/packages/86/6a/1ca0c1a6459e23284debf29907e332ebadda892f1c80add978a28d5bc33c/metator-0.1.1.tar.gz"
            }
        ],
        "0.1.2a0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "ed9325527c3914791f63da98b83508a4",
                    "sha256": "1e32e68f148235db89812f55863871aec01c5f30826933a98a5edeb7d7396f19"
                },
                "downloads": -1,
                "filename": "metator-0.1.2a0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "ed9325527c3914791f63da98b83508a4",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.4",
                "size": 3006681,
                "upload_time": "2018-11-12T00:38:38",
                "url": "https://files.pythonhosted.org/packages/ec/d6/f845a0b2d66ac09d936e02ab0609a29754801c273bc92b2304791270f1ad/metator-0.1.2a0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "af530732502e17a89dacc661565234b9",
                    "sha256": "313f9c7b4ca97f8ce45aeb26dabc1ffdfe64e2ec63272c5355fea7b2aa94f099"
                },
                "downloads": -1,
                "filename": "metator-0.1.2a0.tar.gz",
                "has_sig": false,
                "md5_digest": "af530732502e17a89dacc661565234b9",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.4",
                "size": 2970700,
                "upload_time": "2018-11-12T00:38:41",
                "url": "https://files.pythonhosted.org/packages/a8/a1/e7c1239332361734fc5e5fcf4c5c8cd3d87338b2b4cabf173e862fff29fd/metator-0.1.2a0.tar.gz"
            }
        ],
        "0.1.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "28f2b04bea19ba4f4d14820b23d4f08f",
                    "sha256": "f016d632aa9b8fa65dec5b43b895aec0b48952603119d7e911150836ca9e61f0"
                },
                "downloads": -1,
                "filename": "metator-0.1.3-py2-none-any.whl",
                "has_sig": false,
                "md5_digest": "28f2b04bea19ba4f4d14820b23d4f08f",
                "packagetype": "bdist_wheel",
                "python_version": "py2",
                "requires_python": ">=3.4",
                "size": 2997509,
                "upload_time": "2018-11-12T11:32:08",
                "url": "https://files.pythonhosted.org/packages/95/df/a01e3ae29761dfea9f13c16e17ec14eb39cb91c3831f46523c43ef8256f6/metator-0.1.3-py2-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "55f36802e386459f94d14df081e8105b",
                    "sha256": "e807b7d2797660db7863d3fcbed0fc9adc558f4c5f5387a0b1dd8e32ad3e0ca4"
                },
                "downloads": -1,
                "filename": "metator-0.1.3.tar.gz",
                "has_sig": false,
                "md5_digest": "55f36802e386459f94d14df081e8105b",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.4",
                "size": 2970685,
                "upload_time": "2018-11-12T11:32:11",
                "url": "https://files.pythonhosted.org/packages/dd/dd/df8fe6145a79688c102242e41ad61e0cd5a123b011e4bc62cf353c6a4be1/metator-0.1.3.tar.gz"
            }
        ],
        "0.1.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "a4c052607478572a3414b742e3cb03a9",
                    "sha256": "658617bd0d7611f0c80a2389f38807146f9bdd5847d093f51442dd96540a04e0"
                },
                "downloads": -1,
                "filename": "metator-0.1.4-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "a4c052607478572a3414b742e3cb03a9",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.4",
                "size": 3006779,
                "upload_time": "2018-11-12T14:39:51",
                "url": "https://files.pythonhosted.org/packages/65/89/667cdf04333abf4c1e31e2dbc279358b5271634c619686de4e5f2cceedf9/metator-0.1.4-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "17d1712da2b98341acbe1567a872a1e6",
                    "sha256": "6d95941e5b196783a9c8d0f5dff3720229c97a3f63095383c461d36b3985569a"
                },
                "downloads": -1,
                "filename": "metator-0.1.4.tar.gz",
                "has_sig": false,
                "md5_digest": "17d1712da2b98341acbe1567a872a1e6",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.4",
                "size": 2970874,
                "upload_time": "2018-11-12T14:39:54",
                "url": "https://files.pythonhosted.org/packages/11/ef/9dfaceac6bfa5552a392144fab6cee2262f48c57e73973f9de4e198f6bdc/metator-0.1.4.tar.gz"
            }
        ],
        "0.1.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "492826b80ec0371459860836c6c0bd18",
                    "sha256": "26e30914a7343e7c2997990b6849d7a6f03fb60dceedeb39d4775ece700900d2"
                },
                "downloads": -1,
                "filename": "metator-0.1.5-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "492826b80ec0371459860836c6c0bd18",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.4",
                "size": 3006841,
                "upload_time": "2018-11-12T17:15:01",
                "url": "https://files.pythonhosted.org/packages/4f/a2/d9e534e48b90ebe4282e65e813d78b6507ead2430d9d156d68d67398b665/metator-0.1.5-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "8e2aa26e220f2db0846e149b844ac83f",
                    "sha256": "89f7dbd717fb1da4c65833e20893bd9acf16b510f4162c54e10991e0151f7091"
                },
                "downloads": -1,
                "filename": "metator-0.1.5.tar.gz",
                "has_sig": false,
                "md5_digest": "8e2aa26e220f2db0846e149b844ac83f",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.4",
                "size": 2970950,
                "upload_time": "2018-11-12T17:15:06",
                "url": "https://files.pythonhosted.org/packages/f1/82/2ecca142b0129995b9c9ea4fb0835ac5ca896003b634d4b5e0f716143ba5/metator-0.1.5.tar.gz"
            }
        ],
        "0.1.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b5085c0847aa79954b58d52e41bb6c0d",
                    "sha256": "3862a2d7da3d4982b1f6183879b5a48a815a822e797fe615eaaf6d0853937f70"
                },
                "downloads": -1,
                "filename": "metator-0.1.6-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "b5085c0847aa79954b58d52e41bb6c0d",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.4",
                "size": 3007798,
                "upload_time": "2018-11-22T09:32:50",
                "url": "https://files.pythonhosted.org/packages/3e/4e/51b4cf0369e9ff8bb1650238e8698f9229a1e51b5b3e1e0a6fc7b1981daf/metator-0.1.6-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "0b006d2ecd996e91ff676d94df9b2254",
                    "sha256": "2c2fec7eb31686a05187b14b25fce95804ee3f6a6b3baa93c26e2e03348a4cbc"
                },
                "downloads": -1,
                "filename": "metator-0.1.6.tar.gz",
                "has_sig": false,
                "md5_digest": "0b006d2ecd996e91ff676d94df9b2254",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.4",
                "size": 2971552,
                "upload_time": "2018-11-22T09:33:14",
                "url": "https://files.pythonhosted.org/packages/2b/32/f2a7cc4b3413e49acea06a33558b1501ecf3367a6c0660a828db2cb28fb4/metator-0.1.6.tar.gz"
            }
        ],
        "0.1.7": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "2403a04b0d9cdf626cdb9cc568663cae",
                    "sha256": "71d6eac5de33238a27404861173243c5971f8013c72e1f42486e5c2b79d4cbdc"
                },
                "downloads": -1,
                "filename": "metator-0.1.7-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "2403a04b0d9cdf626cdb9cc568663cae",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.4",
                "size": 3007982,
                "upload_time": "2019-01-24T11:40:27",
                "url": "https://files.pythonhosted.org/packages/d6/f8/030b6b53c6773d8471764af358039284c08e61ea6fd6f97cbe5c1fd41fa8/metator-0.1.7-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "7b318ef9ebe5561d21c5ab6fbfd0df44",
                    "sha256": "eac10da260d2682ad82a8ad09427f06971d90d059c566040c9f1f2c6d1fffd9b"
                },
                "downloads": -1,
                "filename": "metator-0.1.7.tar.gz",
                "has_sig": false,
                "md5_digest": "7b318ef9ebe5561d21c5ab6fbfd0df44",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.4",
                "size": 2971795,
                "upload_time": "2019-01-24T11:41:07",
                "url": "https://files.pythonhosted.org/packages/8d/15/f8135dfee6fe0ed8892a539a51bbc8a17e8e3b63b91eb173e14df074d6e3/metator-0.1.7.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "2403a04b0d9cdf626cdb9cc568663cae",
                "sha256": "71d6eac5de33238a27404861173243c5971f8013c72e1f42486e5c2b79d4cbdc"
            },
            "downloads": -1,
            "filename": "metator-0.1.7-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "2403a04b0d9cdf626cdb9cc568663cae",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=3.4",
            "size": 3007982,
            "upload_time": "2019-01-24T11:40:27",
            "url": "https://files.pythonhosted.org/packages/d6/f8/030b6b53c6773d8471764af358039284c08e61ea6fd6f97cbe5c1fd41fa8/metator-0.1.7-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "7b318ef9ebe5561d21c5ab6fbfd0df44",
                "sha256": "eac10da260d2682ad82a8ad09427f06971d90d059c566040c9f1f2c6d1fffd9b"
            },
            "downloads": -1,
            "filename": "metator-0.1.7.tar.gz",
            "has_sig": false,
            "md5_digest": "7b318ef9ebe5561d21c5ab6fbfd0df44",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.4",
            "size": 2971795,
            "upload_time": "2019-01-24T11:41:07",
            "url": "https://files.pythonhosted.org/packages/8d/15/f8135dfee6fe0ed8892a539a51bbc8a17e8e3b63b91eb173e14df074d6e3/metator-0.1.7.tar.gz"
        }
    ]
}