{
    "info": {
        "author": "Albert Chen",
        "author_email": "chen.alb@husky.neu.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "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 :: Bio-Informatics"
        ],
        "description": "# DART-ID\n\n![GitHub release](https://img.shields.io/github/release/SlavovLab/DART-ID.svg)\n![PyPI](https://img.shields.io/pypi/v/dart-id.svg)\n![PyPI - Downloads](https://img.shields.io/pypi/dm/dart-id.svg)\n![GitHub](https://img.shields.io/github/license/SlavovLab/DART-ID.svg)\n\nWebsite: [https://dart-id.slavovlab.net](https://dart-id.slavovlab.net)\n\nManuscript: [https://www.biorxiv.org/content/10.1101/399121v3](https://www.biorxiv.org/content/10.1101/399121v3)\n\n----------\n\n## Getting started\n\n### Dependencies\n\nDART-ID requires Python >= 3.4 (64-bit - [miniconda distribution recommended](https://docs.conda.io/en/latest/miniconda.html)), and has been tested on Windows 8 / OSX Mojave 10.14 / Centos 7 / Ubuntu 14.04.\n\n### Installation\n\nDART-ID is available on [PyPI](https://pypi.org/project/dart-id/) and can be installed with [pip](https://pip.pypa.io/en/stable/installing/).\n\n```bash\npip install dart-id\n```\n\n### Usage\n\nDART-ID requires a YAML-formatted configuration file to run. An example annotated config file can be found in [example/config_annotated.yaml](https://github.com/SlavovLab/DART-ID/blob/master/example/config_annotated.yaml). You can specify input files and the output folder on the command line, if that's what you prefer.\n\nView the command-line arguments anytime by running: ```dart_id -h```.\n\n```\nusage: dart_id [-h] [-i INPUT [INPUT ...]] [-o OUTPUT] [-v] [--version] -c\n                 CONFIG_FILE\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -i INPUT [INPUT ...], --input INPUT [INPUT ...]\n                        Input file(s) from search engine output (e.g.,\n                        MaxQuant evidence.txt). Not required if input files\n                        are specified in the config file\n  -o OUTPUT, --output OUTPUT\n                        Path to output folder\n  -v, --verbose\n  --version             Display the program's version\n  -c CONFIG_FILE, --config-file CONFIG_FILE\n                        Path to config file (required). See\n                        example/config_example.yaml\n```\n\n### Example runs\n\nAn example configuration file can be downloaded from GitHub: [https://github.com/SlavovLab/DART-ID/blob/master/config_files/example_sqc_67_95_varied.yaml](https://raw.githubusercontent.com/SlavovLab/DART-ID/master/config_files/example_sqc_67_95_varied.yaml).\n\nThe first few lines of the above configuration file specify the path to the input file:\n\n```yaml\n## Input\n## ==========================\n\ninput: \n  - /path/to/SQC_67_95_Varied/evidence.txt\n```\n\nYou can download the ```evidence.txt``` file from MassIVE: [ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/SQC_67_95_Varied/evidence.txt](ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/SQC_67_95_Varied/evidence.txt). \n\nThen edit the path to the file downloaded, and run the following command:\n\n```bash\ndart_id -c config_files/example_sqc_67_95_varied.yaml -o ~/DART_ID/SQC_67_95_varied_20181206\n```\n\nThe ```-o``` parameter points to the output folder for DART-ID. You can also specify this path in the config file.\n\nAn example analysis of the data and configuration file specified above is available publicly at [ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/](ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/). \n\n---\n\n## About the project\n\nDART-ID is a project developed in the [Slavov Laboratory](https://web.northeastern.edu/slavovlab/) at [Northeastern University](https://www.northeastern.edu/) [Bioengineering](http://www.bioe.neu.edu/), and was authored by [Albert Tian Chen](https://atchen.me), [Alexander Franks](http://afranks.com/) (of [UCSB Statistics and Applied Probability](https://www.pstat.ucsb.edu/)), and [Nikolai Slavov](https://web.northeastern.edu/slavovlab/).\n\nThe manuscript for this tool is available on bioRxiv: [https://www.biorxiv.org/content/10.1101/399121v3](https://www.biorxiv.org/content/10.1101/399121v3).\n\nContact the authors by email: [nslavov\\{at\\}northeastern.edu](mailto:nslavov@northeastern.edu).\n\n### License\n\nDART-ID is distributed by an [MIT license](https://github.com/SlavovLab/DART-ID/blob/master/LICENSE.txt).\n\n### Contributing\n\nPlease feel free to contribute to this project by opening an issue or pull request in the [GitHub repository](https://github.com/SlavovLab/DART-ID).\n\n### Data\n\nAll data used for the manuscript is available on [UCSD's MassIVE Repository](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=ed5a1ab37dc34985bbedbf3d9a945535)\n\n### Figures/Analysis\n\nScripts for the figures in the DART-ID manuscript are available in a separate GitHub repository, [https://github.com/SlavovLab/DART-ID_2018](https://github.com/SlavovLab/DART-ID_2018) \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/SlavovLab/DART-ID",
        "keywords": "bayesian retention time psm peptide spectra update",
        "license": "MIT",
        "maintainer": "",
        "maintainer_email": "",
        "name": "dart-id",
        "package_url": "https://pypi.org/project/dart-id/",
        "platform": "",
        "project_url": "https://pypi.org/project/dart-id/",
        "project_urls": {
            "Documentation": "https://github.com/SlavovLab/DART-ID",
            "Homepage": "https://github.com/SlavovLab/DART-ID",
            "Lab Page": "https://web.northeastern.edu/slavovlab/",
            "Source": "https://github.com/SlavovLab/DART-ID",
            "Tracker": "https://github.com/SlavovLab/DART-ID/issues"
        },
        "release_url": "https://pypi.org/project/dart-id/2.0.6/",
        "requires_dist": [
            "pyyaml (>=3.12)",
            "numpy (>=1.14.3)",
            "scipy (>=1.0.0)",
            "pandas (>=0.22.0)",
            "matplotlib (>=2.1.2)",
            "networkx (>=2.1)",
            "jsonschema (>=3.0.1)"
        ],
        "requires_python": "",
        "summary": "RT Alignment and Peptide ID Confidence Updating for LC-MS/MS Data",
        "version": "2.0.6"
    },
    "last_serial": 5329153,
    "releases": {
        "2.0.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "3d4fb3d00d0d925142b17a011bc3696d",
                    "sha256": "52237d86a2903a27735e32c0585c114bb95e60dc6d478ba782879b9dfa1388cb"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "3d4fb3d00d0d925142b17a011bc3696d",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3235014,
                "upload_time": "2019-05-05T19:30:44",
                "url": "https://files.pythonhosted.org/packages/36/2f/64532ae2bbdce540f547ef69b1b67a89dd7af3709209030981c8c14597c8/dart_id-2.0.0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "84181f9147a48458dc1a2c700ac46de6",
                    "sha256": "ecc828f94743a30146142e42f1d3f40b30fb65574bd419753b88168d0de2df0f"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.0.tar.gz",
                "has_sig": false,
                "md5_digest": "84181f9147a48458dc1a2c700ac46de6",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3209512,
                "upload_time": "2019-05-05T19:30:54",
                "url": "https://files.pythonhosted.org/packages/81/2d/0f758a5a438e3b1017179ee32722aec1b3fb4af9d765b0b90238e1542c2b/dart_id-2.0.0.tar.gz"
            }
        ],
        "2.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "ce2d0d4150c332ca18317337cde47172",
                    "sha256": "7ac39141a81930f59082675dcc41870a2ab9be6d9c823c63921ed455d6643ddf"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "ce2d0d4150c332ca18317337cde47172",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3235300,
                "upload_time": "2019-05-08T01:34:19",
                "url": "https://files.pythonhosted.org/packages/e0/d6/0b8f5cf1c56958ef1678ca81e66ccbf1517d816d0e58b14b3d7cfb1fa732/dart_id-2.0.1-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "f7bf4c3e25968ea25cc7310470c29171",
                    "sha256": "fb364f0eff6c32424d8424e338d272a30fd6fa4935272dc9495024bd3d1d05a3"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "f7bf4c3e25968ea25cc7310470c29171",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3209721,
                "upload_time": "2019-05-08T01:34:21",
                "url": "https://files.pythonhosted.org/packages/0f/c7/1da559d2a500d43d1cc2ae62a59948a5640a11fc701b33a9d0b093702771/dart_id-2.0.1.tar.gz"
            }
        ],
        "2.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "cfb262a6e85e62154ac532afb8fbcb59",
                    "sha256": "07f8217e9a97ceaaddd8a2c3a2d48e51a20b2f100cb92d361d2c688b1d3cb54b"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "cfb262a6e85e62154ac532afb8fbcb59",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3236525,
                "upload_time": "2019-05-08T01:57:19",
                "url": "https://files.pythonhosted.org/packages/a1/41/93c0e3d7d50d824a7ab412a9f3025d1cc197e14a0fff183bed6f1ce3ba04/dart_id-2.0.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "ed4715c54d53b699a49e2baf504dfb7b",
                    "sha256": "ecc7e05c9a0eaae01bfe9f03303bb0f479d7ec78aaa9295a419b0eecd06cff72"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "ed4715c54d53b699a49e2baf504dfb7b",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3210565,
                "upload_time": "2019-05-08T01:57:21",
                "url": "https://files.pythonhosted.org/packages/2c/73/90e5168cbb6d20233c5b795657021ec49896e3ed25c80e9fab12bcd513f6/dart_id-2.0.2.tar.gz"
            }
        ],
        "2.0.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "70358695e309ade20d83cafbab1ea755",
                    "sha256": "016a75f85129c822889a1275a71a868b8e432e90a5e502acb879c3bb262f765d"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.3-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "70358695e309ade20d83cafbab1ea755",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3236561,
                "upload_time": "2019-05-10T21:10:29",
                "url": "https://files.pythonhosted.org/packages/c7/86/8026a8c2ba618506d27139a5a508f88990832d5b81100f46eb64ddffce6d/dart_id-2.0.3-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "75084cc476479f5a03fcb241cb1afc71",
                    "sha256": "6e9723e1e6c982bcc4d2d663fcdcc14e9cf2d788c952a17be2503ac5727b2dd5"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.3.tar.gz",
                "has_sig": false,
                "md5_digest": "75084cc476479f5a03fcb241cb1afc71",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3210684,
                "upload_time": "2019-05-10T21:10:31",
                "url": "https://files.pythonhosted.org/packages/8c/31/9209903560ceab1fa1bc8baedcf9d6b4fd0e3315410f60c89b7d18dffc59/dart_id-2.0.3.tar.gz"
            }
        ],
        "2.0.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "110e1877f2b7d2396aa3ff8a9b31070d",
                    "sha256": "dcc548930c4aaad8ff52f7e2ec292abca0d31eab82faee6f6957a4127f890c98"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.4-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "110e1877f2b7d2396aa3ff8a9b31070d",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3237052,
                "upload_time": "2019-05-14T04:17:32",
                "url": "https://files.pythonhosted.org/packages/31/7e/768278ebcf2e205a19e6976a9880d47a7a799257a2800e7432dbd68b4b96/dart_id-2.0.4-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "1feba0b277e2acd811e8afb20ebdc909",
                    "sha256": "24c54fee9cb165e6aad941822fc852bba074ad825351c1c2b24f9f512cfb8d03"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.4.tar.gz",
                "has_sig": false,
                "md5_digest": "1feba0b277e2acd811e8afb20ebdc909",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3210674,
                "upload_time": "2019-05-14T04:17:39",
                "url": "https://files.pythonhosted.org/packages/cb/10/181ac8e58e64542ffa33660980bf8d56daa98437c407a2ec4303106e70f1/dart_id-2.0.4.tar.gz"
            }
        ],
        "2.0.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c3b549978e0ce5b9ba10d374c8fa823e",
                    "sha256": "f6e1972276495d596e3bcc3954417286942aa4851d5a0a97f6be163f6f3ada0f"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.5-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "c3b549978e0ce5b9ba10d374c8fa823e",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3239656,
                "upload_time": "2019-05-22T00:44:20",
                "url": "https://files.pythonhosted.org/packages/d3/d0/274cb484b1593ab97b08ed8cd2986b35a1457a9ee827dbfc9642135625b1/dart_id-2.0.5-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "ca4e709a42a11e8fe33bbd4d643aeb61",
                    "sha256": "6a284efa8be7de833e95ded870f0a7fefa829f54c9bfe83ce771528c8fcdfb6a"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.5.tar.gz",
                "has_sig": false,
                "md5_digest": "ca4e709a42a11e8fe33bbd4d643aeb61",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3211128,
                "upload_time": "2019-05-22T00:44:24",
                "url": "https://files.pythonhosted.org/packages/92/df/a896e0f91d22f67bcb0b9d6ad844ee77f90eabb80cc84536a7c5b149e0d5/dart_id-2.0.5.tar.gz"
            }
        ],
        "2.0.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c33365ec5dd01e8e404430d75d690cef",
                    "sha256": "5e2bcdbffcde3200403cd3825678306405e6c41039bea02390411e69bfd6d957"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.6-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "c33365ec5dd01e8e404430d75d690cef",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 3264755,
                "upload_time": "2019-05-28T21:36:39",
                "url": "https://files.pythonhosted.org/packages/94/c6/2245c0ae54614145e18df09e2d05638f7eb67684ef98f03757ff0b764c16/dart_id-2.0.6-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "fded361a60804d3c49dfc9af426ec96a",
                    "sha256": "0b02dd4050bd1edb1cf2d66792e76db2ba9aa5562ee03086c319bc67b3da04fa"
                },
                "downloads": -1,
                "filename": "dart_id-2.0.6.tar.gz",
                "has_sig": false,
                "md5_digest": "fded361a60804d3c49dfc9af426ec96a",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 3237437,
                "upload_time": "2019-05-28T21:36:42",
                "url": "https://files.pythonhosted.org/packages/7c/de/9b985600071ac88042871bc5210c923926783494a023d40db222797709cf/dart_id-2.0.6.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "c33365ec5dd01e8e404430d75d690cef",
                "sha256": "5e2bcdbffcde3200403cd3825678306405e6c41039bea02390411e69bfd6d957"
            },
            "downloads": -1,
            "filename": "dart_id-2.0.6-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "c33365ec5dd01e8e404430d75d690cef",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": null,
            "size": 3264755,
            "upload_time": "2019-05-28T21:36:39",
            "url": "https://files.pythonhosted.org/packages/94/c6/2245c0ae54614145e18df09e2d05638f7eb67684ef98f03757ff0b764c16/dart_id-2.0.6-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "fded361a60804d3c49dfc9af426ec96a",
                "sha256": "0b02dd4050bd1edb1cf2d66792e76db2ba9aa5562ee03086c319bc67b3da04fa"
            },
            "downloads": -1,
            "filename": "dart_id-2.0.6.tar.gz",
            "has_sig": false,
            "md5_digest": "fded361a60804d3c49dfc9af426ec96a",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 3237437,
            "upload_time": "2019-05-28T21:36:42",
            "url": "https://files.pythonhosted.org/packages/7c/de/9b985600071ac88042871bc5210c923926783494a023d40db222797709cf/dart_id-2.0.6.tar.gz"
        }
    ]
}