magpurify2


Namemagpurify2 JSON
Version 1.0.2 PyPI version JSON
download
home_pagehttps://github.com/apcamargo/magpurify2/
SummaryIdentify and remove contaminants from metagenome-assembled genomes.
upload_time2023-05-16 02:58:08
maintainer
docs_urlNone
authorAntonio Camargo
requires_python>=3.6
licenseGNU General Public License v3.0
keywords bioinformatics metagenomics metagenome-assembled genomes
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            <img src="https://raw.githubusercontent.com/apcamargo/magpurify2/master/website/.vuepress/public/logo_without_type.svg?token=AFPA2JEOQW3DH6XWN62XPGC6YH3HQ" align="left" width="200" height="150px"/>
<img align="left" width="0" height="150px" hspace="0"/>

Improve the quality of metagenome-assembled genomes by identifying and removing contaminant sequences with an easy-to-use and modular command-line interface.

[![MIT License](https://img.shields.io/badge/license-MIT-007EC7.svg?style=flat-square)](/LICENSE) [![Fish Shell Version](https://img.shields.io/badge/fish-≥v2.2.0-007EC7.svg?style=flat-square)](http://fishshell.com) [![Travis Build Status](http://img.shields.io/travis/oh-my-fish/oh-my-fish.svg?style=flat-square)](https://travis-ci.org/oh-my-fish/oh-my-fish)

You can find MAGpurify2's full documentation at its [website](https://apcamargo.github.io/magpurify2/).

---

## Quick start


Download test data:

```bash
fileId="1-Gf-FsVIcARqrUb-LHS_FZlb-sCGAmfo"
fileName="magpurify2_test_data.tar.gz"
curl -sc /tmp/cookie "https://drive.google.com/uc?export=download&id=${fileId}" > /dev/null
code="$(awk '/_warning_/ {print $NF}' /tmp/cookie)"
curl -Lb /tmp/cookie "https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}" -o ${fileName}
tar zxfv magpurify2_test_data.tar.gz
```

Download database:

```bash
fileId="1ooWiR3LplBy5GsY5wZ7o6dwswiCWVvmi"
fileName="magpurify2DB.v1.0.tar.gz"
curl -sc /tmp/cookie "https://drive.google.com/uc?export=download&id=${fileId}" > /dev/null
code="$(awk '/_warning_/ {print $NF}' /tmp/cookie)"
curl -Lb /tmp/cookie "https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}" -o ${fileName}
tar zxfv magpurify2DB.v1.0.tar.gz
```

Execute the pipeline:

```bash
magpurify2 composition test_data/genomes/* output
magpurify2 coverage test_data/genomes/* output --bam_files test_data/bam_files/*
magpurify2 taxonomy test_data/genomes/* output magpurify2DB
magpurify2 filter test_data/genomes/* output filtered_genomes
```

Raw data

            {
    "_id": null,
    "home_page": "https://github.com/apcamargo/magpurify2/",
    "name": "magpurify2",
    "maintainer": "",
    "docs_url": null,
    "requires_python": ">=3.6",
    "maintainer_email": "",
    "keywords": "bioinformatics,metagenomics,metagenome-assembled genomes",
    "author": "Antonio Camargo",
    "author_email": "antoniop.camargo@gmail.com",
    "download_url": "",
    "platform": null,
    "description": "<img src=\"https://raw.githubusercontent.com/apcamargo/magpurify2/master/website/.vuepress/public/logo_without_type.svg?token=AFPA2JEOQW3DH6XWN62XPGC6YH3HQ\" align=\"left\" width=\"200\" height=\"150px\"/>\n<img align=\"left\" width=\"0\" height=\"150px\" hspace=\"0\"/>\n\nImprove the quality of metagenome-assembled genomes by identifying and removing contaminant sequences with an easy-to-use and modular command-line interface.\n\n[![MIT License](https://img.shields.io/badge/license-MIT-007EC7.svg?style=flat-square)](/LICENSE) [![Fish Shell Version](https://img.shields.io/badge/fish-\u2265v2.2.0-007EC7.svg?style=flat-square)](http://fishshell.com) [![Travis Build Status](http://img.shields.io/travis/oh-my-fish/oh-my-fish.svg?style=flat-square)](https://travis-ci.org/oh-my-fish/oh-my-fish)\n\nYou can find MAGpurify2's full documentation at its [website](https://apcamargo.github.io/magpurify2/).\n\n---\n\n## Quick start\n\n\nDownload test data:\n\n```bash\nfileId=\"1-Gf-FsVIcARqrUb-LHS_FZlb-sCGAmfo\"\nfileName=\"magpurify2_test_data.tar.gz\"\ncurl -sc /tmp/cookie \"https://drive.google.com/uc?export=download&id=${fileId}\" > /dev/null\ncode=\"$(awk '/_warning_/ {print $NF}' /tmp/cookie)\"\ncurl -Lb /tmp/cookie \"https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}\" -o ${fileName}\ntar zxfv magpurify2_test_data.tar.gz\n```\n\nDownload database:\n\n```bash\nfileId=\"1ooWiR3LplBy5GsY5wZ7o6dwswiCWVvmi\"\nfileName=\"magpurify2DB.v1.0.tar.gz\"\ncurl -sc /tmp/cookie \"https://drive.google.com/uc?export=download&id=${fileId}\" > /dev/null\ncode=\"$(awk '/_warning_/ {print $NF}' /tmp/cookie)\"\ncurl -Lb /tmp/cookie \"https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}\" -o ${fileName}\ntar zxfv magpurify2DB.v1.0.tar.gz\n```\n\nExecute the pipeline:\n\n```bash\nmagpurify2 composition test_data/genomes/* output\nmagpurify2 coverage test_data/genomes/* output --bam_files test_data/bam_files/*\nmagpurify2 taxonomy test_data/genomes/* output magpurify2DB\nmagpurify2 filter test_data/genomes/* output filtered_genomes\n```\n",
    "bugtrack_url": null,
    "license": "GNU General Public License v3.0",
    "summary": "Identify and remove contaminants from metagenome-assembled genomes.",
    "version": "1.0.2",
    "project_urls": {
        "Homepage": "https://github.com/apcamargo/magpurify2/"
    },
    "split_keywords": [
        "bioinformatics",
        "metagenomics",
        "metagenome-assembled genomes"
    ],
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "b516b7412ae21ba9a62430f9d1bf71bf188f9becd3f65004a3a005a87936726f",
                "md5": "fbe8c72d4c524fe6bf438214713b3921",
                "sha256": "5f5c1da930b3248bf802b9d137176c63a2827f4a1059759e1d2cd2184b010ef5"
            },
            "downloads": -1,
            "filename": "magpurify2-1.0.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "has_sig": false,
            "md5_digest": "fbe8c72d4c524fe6bf438214713b3921",
            "packagetype": "bdist_wheel",
            "python_version": "cp310",
            "requires_python": ">=3.6",
            "size": 6247637,
            "upload_time": "2023-05-16T02:58:08",
            "upload_time_iso_8601": "2023-05-16T02:58:08.755114Z",
            "url": "https://files.pythonhosted.org/packages/b5/16/b7412ae21ba9a62430f9d1bf71bf188f9becd3f65004a3a005a87936726f/magpurify2-1.0.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "2c9386fd9493e96c5b9484b92fc888c808fa4ec635da74a58a1f8e514839b9e2",
                "md5": "ba4cd308b7757e21dcc1007fe8596b9f",
                "sha256": "b4eb961eb603e5d1c24db0dcda0d3933677f9669078f254229ae81f79791f74c"
            },
            "downloads": -1,
            "filename": "magpurify2-1.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "has_sig": false,
            "md5_digest": "ba4cd308b7757e21dcc1007fe8596b9f",
            "packagetype": "bdist_wheel",
            "python_version": "cp311",
            "requires_python": ">=3.6",
            "size": 6247636,
            "upload_time": "2023-05-16T03:20:38",
            "upload_time_iso_8601": "2023-05-16T03:20:38.877473Z",
            "url": "https://files.pythonhosted.org/packages/2c/93/86fd9493e96c5b9484b92fc888c808fa4ec635da74a58a1f8e514839b9e2/magpurify2-1.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "0013982ea884ca67510c5efaa786766b247d7bce1f9a634d066c76e7d7f1781e",
                "md5": "84e6b6d1090168d167826f8e54e11da0",
                "sha256": "2ebd97ccdac49b77182cb0a7a8ec5142140854d4223e75dc0334e4b4dad423f1"
            },
            "downloads": -1,
            "filename": "magpurify2-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "has_sig": false,
            "md5_digest": "84e6b6d1090168d167826f8e54e11da0",
            "packagetype": "bdist_wheel",
            "python_version": "cp37",
            "requires_python": ">=3.6",
            "size": 6248052,
            "upload_time": "2023-05-16T02:58:11",
            "upload_time_iso_8601": "2023-05-16T02:58:11.734986Z",
            "url": "https://files.pythonhosted.org/packages/00/13/982ea884ca67510c5efaa786766b247d7bce1f9a634d066c76e7d7f1781e/magpurify2-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "c19a92d9124ca988aa1560de1076b2ae9a1d54630c018243ac3229f467d4c92d",
                "md5": "d3707c1bef066ec6e861af98fb61f7de",
                "sha256": "9f6107d0b29b69dc7e85d5d4f2ae3b81daf9493e69a572dee7e481afe0d7ece4"
            },
            "downloads": -1,
            "filename": "magpurify2-1.0.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "has_sig": false,
            "md5_digest": "d3707c1bef066ec6e861af98fb61f7de",
            "packagetype": "bdist_wheel",
            "python_version": "cp38",
            "requires_python": ">=3.6",
            "size": 6247626,
            "upload_time": "2023-05-16T02:58:14",
            "upload_time_iso_8601": "2023-05-16T02:58:14.677354Z",
            "url": "https://files.pythonhosted.org/packages/c1/9a/92d9124ca988aa1560de1076b2ae9a1d54630c018243ac3229f467d4c92d/magpurify2-1.0.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "2ca2ef8aca5ace8e6c2630809370844a74e0a4945b78870947f2e3721912e033",
                "md5": "4c232d02eb7a5764f90c6ff4016da642",
                "sha256": "677844df8f8a0772f09ff1395b1e78e32ae6b0b992cbd7139d4047ed99a7dce7"
            },
            "downloads": -1,
            "filename": "magpurify2-1.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "has_sig": false,
            "md5_digest": "4c232d02eb7a5764f90c6ff4016da642",
            "packagetype": "bdist_wheel",
            "python_version": "cp39",
            "requires_python": ">=3.6",
            "size": 6247624,
            "upload_time": "2023-05-16T02:58:18",
            "upload_time_iso_8601": "2023-05-16T02:58:18.001080Z",
            "url": "https://files.pythonhosted.org/packages/2c/a2/ef8aca5ace8e6c2630809370844a74e0a4945b78870947f2e3721912e033/magpurify2-1.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
            "yanked": false,
            "yanked_reason": null
        }
    ],
    "upload_time": "2023-05-16 02:58:08",
    "github": true,
    "gitlab": false,
    "bitbucket": false,
    "codeberg": false,
    "github_user": "apcamargo",
    "github_project": "magpurify2",
    "travis_ci": false,
    "coveralls": false,
    "github_actions": true,
    "lcname": "magpurify2"
}
Antonio Camargo
Elapsed time: 0.07453s