{
    "info": {
        "author": "Leighton Pritchard",
        "author_email": "leighton.pritchard@hutton.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# README.md - `ncfp`\n\nThis repository contains code for a script that identifies and writes the corresponding nucleotide sequences for each protein in an input multiple sequence file to be used, for example, in backthreading coding sequences onto protein alignments for phylogenetic analyses. `ncfp` uses the NCBI accession or UniProt gene name (as appropriate) to identify source nucleotide sequences in the NCBI databases, download them, and write them to a file.\n\n[![ncfp TravisCI build status](https://api.travis-ci.org/widdowquinn/ncfp.svg?branch=master)](https://travis-ci.org/widdowquinn/ncfp/branches)\n[![ncfp codecov.io coverage](https://img.shields.io/codecov/c/github/widdowquinn/ncfp/master.svg)](https://codecov.io/github/widdowquinn/ncfp)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/99a037e5eb2c4ae48e27e44c8974a3f8)](https://www.codacy.com/app/widdowquinn/ncfp?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=widdowquinn/ncfp&amp;utm_campaign=Badge_Grade)\n[![ncfp documentation](https://readthedocs.org/projects/ncfp/badge/?version=latest)](https://ncfp.readthedocs.io/en/latest/?badge=latest)\n\n[![ncfp PyPi version](https://img.shields.io/pypi/v/ncfp.svg \"PyPi version\")](https://pypi.python.org/pypi/ncfp)\n[![ncfp licence](https://img.shields.io/pypi/l/ncfp.svg \"PyPi licence\")](https://github.com/widdowquinn/ncfp/blob/master/LICENSE)\n\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/ncfp/badges/version.svg)](https://anaconda.org/bioconda/ncfp)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/ncfp/badges/latest_release_date.svg)](https://anaconda.org/bioconda/ncfp)\n\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/ncfp/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/ncfp/badges/downloads.svg)](https://anaconda.org/bioconda/ncfp)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/ncfp/badges/platforms.svg)](https://anaconda.org/bioconda/ncfp)\n\n\n## Quickstart: `ncfp` at the command-line\n\nProviding an input file of protein sequences as `<INPUT>.fasta`, and writing output to the directory `<OUTPUT>`, while specifying a user email to NCBI of `<EMAIL>` will generate two files: `<OUTPUT>/ncfp_aa.fasta` and `<OUTPUT>/ncfp_nt.fasta`.\n\n```bash\nncfp <INPUT>.fasta <OUTPUT> <EMAIL>\n```\n\nThe file `<OUTPUT>/ncfp_aa.fasta` contains the amino acid sequences for all input proteins for which a corresponding nucleotide coding sequence could be identified, in FASTA format.\n\nThe file `<OUTPUT>/ncfp_nt.fasta` contains nucleotide coding sequences, where they could be found, for all the input proteins, in FASTA format.\n\nAny input protein sequences for which a corresponding nucleotide sequence cannot be recovered, for any reason, are placed in the file `<OUTPUT>/skipped.fas`.\n\nTo find out more about what `ncfp` can do, try\n\n```bash\nncfp --help\n```\n\nat the command-line\n\n## Documentation\n\nFor more detailed information about `ncfp` as a program, or using the underlying `ncbi_cds_from_protein` Python module, please see the most recent documentation at <https://ncfp.readthedocs.io/en/latest/>\n\n## License\n\nUnless otherwise indicated, all code is licensed under the MIT license and subject to the following agreement:\n\n    (c) The James Hutton Institute 2017-2018\n    Author: Leighton Pritchard\n\n    Contact: leighton.pritchard@hutton.ac.uk\n\n    Address:\n    Leighton Pritchard,\n    Information and Computational Sciences,\n    James Hutton Institute,\n    Errol Road,\n    Invergowrie,\n    Dundee,\n    DD2 5DA,\n    Scotland,\n    UK\n\nThe MIT License\n\nCopyright (c) 2017-2018 The James Hutton Institute\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.\n\n\n",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "https://github.com/widdowquinn/ncfp/releases",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "http://widdowquinn.github.io/ncfp/",
        "keywords": "genome bioinformatics sequence",
        "license": "MIT",
        "maintainer": "",
        "maintainer_email": "",
        "name": "ncfp",
        "package_url": "https://pypi.org/project/ncfp/",
        "platform": "Posix; MacOS X",
        "project_url": "https://pypi.org/project/ncfp/",
        "project_urls": {
            "Download": "https://github.com/widdowquinn/ncfp/releases",
            "Homepage": "http://widdowquinn.github.io/ncfp/"
        },
        "release_url": "https://pypi.org/project/ncfp/0.1.1/",
        "requires_dist": [
            "biopython",
            "tqdm"
        ],
        "requires_python": "~=3.5",
        "summary": "ncfp is a script and module that facilitates recovery of nucleotide sequences from NCBI encoding a specified set of input protein sequences",
        "version": "0.1.1"
    },
    "last_serial": 4377861,
    "releases": {
        "0.1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b90e5060ea1fddc2a6b9bef89bd3d5c1",
                    "sha256": "32b439a3c24c99f40ac7828de5961b9c764c2dd8237af287ed3341102039218a"
                },
                "downloads": -1,
                "filename": "ncfp-0.1.0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "b90e5060ea1fddc2a6b9bef89bd3d5c1",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": "~=3.5",
                "size": 22833,
                "upload_time": "2018-02-09T18:11:22",
                "url": "https://files.pythonhosted.org/packages/d3/92/32acb4cf10ca81aa31d377255169cd2d7dff96d6730a0ce5af0b9f0090b3/ncfp-0.1.0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "4ddd2be47b932f4043eb01df9ad5d471",
                    "sha256": "a3af0757660cc61d33a8a20fae9ed1e28d60441517a61312740410a4cc00d74b"
                },
                "downloads": -1,
                "filename": "ncfp-0.1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "4ddd2be47b932f4043eb01df9ad5d471",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.5",
                "size": 15248,
                "upload_time": "2018-02-09T18:11:25",
                "url": "https://files.pythonhosted.org/packages/aa/ae/399662df6cb31eb0b76f324557d9cb15657a2ca7753ee54aeb0d5153475f/ncfp-0.1.0.tar.gz"
            }
        ],
        "0.1.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "9cc99c7d440fa4f7fd8fddbe060b81ee",
                    "sha256": "4a22423fd655f3cc71d0a890126577e3b6944ad71843798af4e230d4a994b928"
                },
                "downloads": -1,
                "filename": "ncfp-0.1.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "9cc99c7d440fa4f7fd8fddbe060b81ee",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": "~=3.5",
                "size": 24167,
                "upload_time": "2018-10-15T15:10:36",
                "url": "https://files.pythonhosted.org/packages/48/f0/93d8c6ffaa914434b3213f13afb21568c6597dc229c39967f63e78d950dd/ncfp-0.1.1-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "8c417b958ca46ff0b683621440312dc3",
                    "sha256": "173ce1acfdef08e9174fc5a943c8d704c14d90f7e4bbe0321218c2f467a7d40e"
                },
                "downloads": -1,
                "filename": "ncfp-0.1.1.tar.gz",
                "has_sig": false,
                "md5_digest": "8c417b958ca46ff0b683621440312dc3",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": "~=3.5",
                "size": 15649,
                "upload_time": "2018-10-15T15:10:37",
                "url": "https://files.pythonhosted.org/packages/82/2a/028434669c6c57f3720b3a98ffb4f8fbaa6653d7438b468391998abbac3f/ncfp-0.1.1.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "9cc99c7d440fa4f7fd8fddbe060b81ee",
                "sha256": "4a22423fd655f3cc71d0a890126577e3b6944ad71843798af4e230d4a994b928"
            },
            "downloads": -1,
            "filename": "ncfp-0.1.1-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "9cc99c7d440fa4f7fd8fddbe060b81ee",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": "~=3.5",
            "size": 24167,
            "upload_time": "2018-10-15T15:10:36",
            "url": "https://files.pythonhosted.org/packages/48/f0/93d8c6ffaa914434b3213f13afb21568c6597dc229c39967f63e78d950dd/ncfp-0.1.1-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "8c417b958ca46ff0b683621440312dc3",
                "sha256": "173ce1acfdef08e9174fc5a943c8d704c14d90f7e4bbe0321218c2f467a7d40e"
            },
            "downloads": -1,
            "filename": "ncfp-0.1.1.tar.gz",
            "has_sig": false,
            "md5_digest": "8c417b958ca46ff0b683621440312dc3",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": "~=3.5",
            "size": 15649,
            "upload_time": "2018-10-15T15:10:37",
            "url": "https://files.pythonhosted.org/packages/82/2a/028434669c6c57f3720b3a98ffb4f8fbaa6653d7438b468391998abbac3f/ncfp-0.1.1.tar.gz"
        }
    ]
}