{
    "info": {
        "author": "Benjamin Lee",
        "author_email": "benjamin_lee@college.harvard.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Science/Research",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "Python Codon Adaptation Index\n=============================\n|DOI| |Docs| |Travis| |CodeFactor| |PyPI|\n\nAn implementation of `Sharp and Li's 1987\nformulation <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC340524/pdf/nar00247-0410.pdf>`_\nof the `codon adaption index\n<https://en.wikipedia.org/wiki/Codon_Adaptation_Index>`_.\n\nInstallation\n------------\n\nThis module is available from PyPI and can be downloaded with the following command::\n\n\t$ pip install CAI\n\nTo install the latest development version::\n\n\t$ pip install git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git\n\n.. _quickstart:\n\nQuickstart\n----------\n\nFinding the CAI of a sequence is easy::\n\n\t>>> from CAI import CAI\n\t>>> CAI(\"ATG...\", reference=[\"ATGTTT...\", \"ATGCGC...\",...])\n\t0.24948128951724224\n\nSimilarly, from the command line::\n\n\t$ CAI -s sequence.fasta -r reference_sequences.fasta\n\t0.24948128951724224\n\nDetermining which sequences to use as the reference set is left to the user,\nthough the `HEG-DB <http://genomes.urv.cat/HEG-DB/>`_ is a great resource of\nhighly expressed genes.\n\nContributing and Getting Support\n--------------------------------\n\nIf you encounter any issues using CAI, feel free to `create an issue\n<https://github.com/Benjamin-Lee/CodonAdaptationIndex/issues>`_.\n\nTo contribute to the project, please `create a pull request\n<https://github.com/Benjamin-Lee/CodonAdaptationIndex/pulls>`_. For more\ninformation on how to do so, please look at GitHub's `documentation on pull\nrequests <https://help.github.com/articles/about-pull-requests>`_.\n\nCitation\n--------\n\nLee, B. D. (2018). Python Implementation of Codon Adaptation Index. *Journal of\nOpen Source Software, 3*(30), 905. `https://doi.org/10.21105/joss.00905\n<https://doi.org/10.21105/joss.00905>`_\n\n```\n@article{Lee2018,\n  doi = {10.21105/joss.00905},\n  url = {https://doi.org/10.21105/joss.00905},\n  year  = {2018},\n  month = {oct},\n  publisher = {The Open Journal},\n  volume = {3},\n  number = {30},\n  pages = {905},\n  author = {Benjamin D. Lee},\n  title = {Python Implementation of Codon Adaptation Index},\n  journal = {Journal of Open Source Software}\n}\n```\n\nContact\n-------\n\nI'm available for contact at\n`benjamin_lee@college.harvard.edu <mailto:benjamin_lee@college.harvard.edu>`_.\n\nReference\n---------\n\nSharp, P. M., & Li, W. H. (1987). The codon adaptation index--a measure of\ndirectional synonymous codon usage bias, and its potential applications.\n*Nucleic Acids Research*, 15(3), 1281\u20131295.\n\n.. |DOI| image:: http://joss.theoj.org/papers/8adf6bd9fd6391d5343d15ea0b6b6525/status.svg\n\t:target: http://joss.theoj.org/papers/8adf6bd9fd6391d5343d15ea0b6b6525\n\n.. |Docs| image:: https://readthedocs.org/projects/cai/badge/?version=latest\n\t:target: https://cai.readthedocs.io/en/latest/?badge=latest\n\t:alt: Documentation Status\n\n.. |Travis| image:: https://travis-ci.org/Benjamin-Lee/CodonAdaptationIndex.svg?branch=master\n\t:target: https://travis-ci.org/Benjamin-Lee/CodonAdaptationIndex\n\n.. |CodeFactor| image:: https://www.codefactor.io/repository/github/benjamin-lee/codonadaptationindex/badge/master\n\t:target: https://www.codefactor.io/repository/github/benjamin-lee/codonadaptationindex/overview/master\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/CAI.svg\n\t:target: https://pypi.org/project/CAI/\n",
        "description_content_type": "",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/Benjamin-Lee/CodonAdaptationIndex",
        "keywords": "",
        "license": "MIT",
        "maintainer": "",
        "maintainer_email": "",
        "name": "CAI",
        "package_url": "https://pypi.org/project/CAI/",
        "platform": "",
        "project_url": "https://pypi.org/project/CAI/",
        "project_urls": {
            "Homepage": "https://github.com/Benjamin-Lee/CodonAdaptationIndex"
        },
        "release_url": "https://pypi.org/project/CAI/1.0.3/",
        "requires_dist": null,
        "requires_python": "",
        "summary": "Python implementation of codon adaptation index",
        "version": "1.0.3"
    },
    "last_serial": 4362349,
    "releases": {
        "0.1.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "03f60683e54b44e38ea1becc61f422ce",
                    "sha256": "278c33602b2117066790bdaeeafb91828e52df0f5f0c84c12bc5ca5827ef38b1"
                },
                "downloads": -1,
                "filename": "CAI-0.1.6.tar.gz",
                "has_sig": false,
                "md5_digest": "03f60683e54b44e38ea1becc61f422ce",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 4825,
                "upload_time": "2017-08-16T08:46:18",
                "url": "https://files.pythonhosted.org/packages/38/54/f9baba1f81b93bcd453977cb0dcce2de329774ad14e38f66d157505855dd/CAI-0.1.6.tar.gz"
            }
        ],
        "0.1.7": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "927d10ec13561957ce33a207ac3d0760",
                    "sha256": "24ff2da54a25aac8dc2c3211a8ff69091de5d4e446ba3c749b3d482be1c048f1"
                },
                "downloads": -1,
                "filename": "CAI-0.1.7.tar.gz",
                "has_sig": false,
                "md5_digest": "927d10ec13561957ce33a207ac3d0760",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 4855,
                "upload_time": "2017-08-18T04:31:18",
                "url": "https://files.pythonhosted.org/packages/48/e9/6134097aac388837ad5398fd5676aa1e5568fb2a97b459a6e4d5d25257e9/CAI-0.1.7.tar.gz"
            }
        ],
        "0.1.8": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "ad552e8d03844a9c7ca26940371883b8",
                    "sha256": "ae60067b20e392cbb187968f5b6bf19d9d66d186ba9a7d7f2c5588d6259bb452"
                },
                "downloads": -1,
                "filename": "CAI-0.1.8.tar.gz",
                "has_sig": false,
                "md5_digest": "ad552e8d03844a9c7ca26940371883b8",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 6238,
                "upload_time": "2017-12-30T15:08:58",
                "url": "https://files.pythonhosted.org/packages/88/0e/5a0332221bbd81d23081caf58b8255a2bc490c09463ba2f13931caf74f1b/CAI-0.1.8.tar.gz"
            }
        ],
        "1.0.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "61cb45e95905479ff7d8e8aee781c87b",
                    "sha256": "abc19a36caed4331926eaa401cc0bddd9de5688f4147eb060a3b06d6d8234137"
                },
                "downloads": -1,
                "filename": "CAI-1.0.0.tar.gz",
                "has_sig": false,
                "md5_digest": "61cb45e95905479ff7d8e8aee781c87b",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5343,
                "upload_time": "2018-06-06T18:12:12",
                "url": "https://files.pythonhosted.org/packages/ba/30/45d2293d937b49475aa8ac7ab1e970ae08f74aef29f562d777e15deffe6d/CAI-1.0.0.tar.gz"
            }
        ],
        "1.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "31d86ee1f54e91245cef797df4251e49",
                    "sha256": "91db783bef548bc58f1957ccac5224b6925fc9462dae5d3c9e6dfe62eebbdbdf"
                },
                "downloads": -1,
                "filename": "CAI-1.0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "31d86ee1f54e91245cef797df4251e49",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5410,
                "upload_time": "2018-08-22T20:28:41",
                "url": "https://files.pythonhosted.org/packages/52/65/f99b121275b078390ba324f4221d1375a99bbcf98bdcf20e3fcb7b583c18/CAI-1.0.1.tar.gz"
            }
        ],
        "1.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b07e614c828e1f153c803c3a97c1f61b",
                    "sha256": "93dd6d603afd3c75d5cdb6fb6b9e2f49f136a5f62487e493ae2bc82ed620e3bf"
                },
                "downloads": -1,
                "filename": "CAI-1.0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "b07e614c828e1f153c803c3a97c1f61b",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5771,
                "upload_time": "2018-10-01T02:04:06",
                "url": "https://files.pythonhosted.org/packages/78/69/20f57c4a2f1d27653f1628eda1c5eb935c7cbd3f0a21abd7c4738a0eda09/CAI-1.0.2.tar.gz"
            }
        ],
        "1.0.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "cffb1359737459f69f709c6325ba4836",
                    "sha256": "48304d0e057213764c07d6b46292d35695248c4b88d23f8633c07fe138ef9287"
                },
                "downloads": -1,
                "filename": "CAI-1.0.3.tar.gz",
                "has_sig": false,
                "md5_digest": "cffb1359737459f69f709c6325ba4836",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 6040,
                "upload_time": "2018-10-11T01:37:51",
                "url": "https://files.pythonhosted.org/packages/26/a5/7ec1c5f63dfd0bbeaf76131394a35decf4369cf7708dcb5935ea3cd51766/CAI-1.0.3.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "cffb1359737459f69f709c6325ba4836",
                "sha256": "48304d0e057213764c07d6b46292d35695248c4b88d23f8633c07fe138ef9287"
            },
            "downloads": -1,
            "filename": "CAI-1.0.3.tar.gz",
            "has_sig": false,
            "md5_digest": "cffb1359737459f69f709c6325ba4836",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 6040,
            "upload_time": "2018-10-11T01:37:51",
            "url": "https://files.pythonhosted.org/packages/26/a5/7ec1c5f63dfd0bbeaf76131394a35decf4369cf7708dcb5935ea3cd51766/CAI-1.0.3.tar.gz"
        }
    ]
}