{
    "info": {
        "author": "David Lawrence",
        "author_email": "davmlaw@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Programming Language :: Python :: 3.9"
        ],
        "description": "## PyReference ##\n\n[![PyPi version](https://img.shields.io/pypi/v/pyreference.svg)](https://pypi.org/project/pyreference/) [![Python versions](https://img.shields.io/pypi/pyversions/pyreference.svg)](https://pypi.org/project/pyreference/) [![PyReference](https://img.shields.io/pypi/dm/pyreference.svg)](https://pypi.org/project/pyreference/)\n\nA Python library for working with reference gene annotations.\n\nPyReference loads GTF annotations extremely rapidly, and makes it easy to write code which can be run against different genomes.\n\n## Example ##\n\n    import numpy as np\n    import pyreference\n\t\n\treference = pyreference.Reference()\n\n\tmy_gene_ids = [\"MSN\", \"GATA2\", \"ZEB1\"]\n\tfor gene in reference[my_gene_ids]:\n\t\taverage_length = np.mean([t.length for t in gene.transcripts])\n\t\tprint(\"%s average length = %.2f\" % (gene, average_length))\n\t\tprint(gene.iv)\n\t\tfor transcript in gene.transcripts:\n\t\t\tif transcript.is_coding:\n\t\t\t\tthreep_utr = transcript.get_3putr_sequence()\n\t\t\t\tprint(\"%s end of 3putr: %s\" % (transcript.get_id(), threep_utr[-20:]))\n\nOutputs:\n\n\tMSN (MSN) 1 transcripts average length = 3970.00\n\tchrX:[64887510,64961793)/+\n\tNM_002444 end of 3putr: TAAAATTTAGGAAGACTTCA\n\n\tGATA2 (GATA2) 3 transcripts average length = 3367.67\n\tchr3:[128198264,128212030)/-\n\tNM_001145662 end of 3putr: AATACTTTTTGTGAATGCCC\n\tNM_001145661 end of 3putr: AATACTTTTTGTGAATGCCC\n\tNM_032638 end of 3putr: AATACTTTTTGTGAATGCCC\n\n\tZEB1 (ZEB1) 6 transcripts average length = 6037.83\n\tchr10:[31608100,31818742)/+\n\tNM_001174093 end of 3putr: CTTCTTTTTCTATTGCCTTA\n\tNM_001174094 end of 3putr: CTTCTTTTTCTATTGCCTTA\n\tNM_030751 end of 3putr: CTTCTTTTTCTATTGCCTTA\n\tNM_001174096 end of 3putr: CTTCTTTTTCTATTGCCTTA\n\tNM_001174095 end of 3putr: CTTCTTTTTCTATTGCCTTA\n\tNM_001128128 end of 3putr: CTTCTTTTTCTATTGCCTTA\n\nThis takes less than 4 seconds to load via a network drive on my machine.\n\n## Installation ##\n\n    sudo pip install pyreference\n\nChoose your annotation:\n\n    # Latest Ensembl GRCh37\n    wget ftp://ftp.ensembl.org/pub/grch37/release-87/gff3/homo_sapiens/Homo_sapiens.GRCh37.87.gff3.gz\n\n    # Latest Ensembl GRCh38\n    wget ftp://ftp.ensembl.org/pub/release-104/gff3/homo_sapiens/Homo_sapiens.GRCh38.104.gff3.gz\n\n    # Latest RefSeq GRCh37\n    wget http://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/105.20201022/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz\n\n    # Latest RefSeq GRCh38\n    http://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/109.20210514/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz\n\nPre-process your GFF3 or GTF files to create genes.gtf.json.gz (~1/20th the size of the input GTF file)\n    \n    pyreference_gff_to_json.py --gff3 genes.gff.gz\n\nCreate a ~/pyreference.cfg file pointing to your references.\n\n\t[global]\n\tdefault_build=hg19\n\n\t[hg19]\n\tgenes_json=/data/reference/hg19/genes.gtf.json.gz\n\tmature_mir_sequence_fasta=/data/reference/hg19/mature.fa\n\tgenome_sequence_fasta=/data/reference/hg19/genome.fa\n\n\t[mm10]\n\tgenes_json=/data/reference/mm10/genes.gtf.json.gz\n\tmature_mir_sequence_fasta=/data/reference/mm10/mature.fa\n\tgenome_sequence_fasta=/data/reference/mm10/genome.fa\n\n\n## Command line arguments ##\n\nSubstitute ArgumentParser with pyreference.ReferenceArgumentParser to add a --build option to your command line arguments. \n\nargs.reference is now initialised to the correct build/annotation.\n\n\tfrom pyreference import ReferenceArgumentParser\n\n\tparser = ReferenceArgumentParser()\n\tparser.add(\"mirna_name\")\n\n\targs = parser.parse_args()\n\treference = args.reference.get_mirna(args.mirna_name)\n\tprint(mir.get_8mer_target())\n\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/SACGF/pyreference",
        "keywords": "genomics,gtf,gff,genome,genes",
        "license": "",
        "maintainer": "",
        "maintainer_email": "",
        "name": "pyreference",
        "package_url": "https://pypi.org/project/pyreference/",
        "platform": "",
        "project_url": "https://pypi.org/project/pyreference/",
        "project_urls": {
            "Homepage": "https://github.com/SACGF/pyreference"
        },
        "release_url": "https://pypi.org/project/pyreference/0.6.3/",
        "requires_dist": [
            "numpy",
            "biopython",
            "configargparse",
            "deprecation",
            "HTSeq",
            "lazy",
            "pysam",
            "pandas",
            "seaborn"
        ],
        "requires_python": ">=2.7, >=3.5",
        "summary": "Library for working with reference genomes and gene GTF/GFFs",
        "version": "0.6.3",
        "yanked": false,
        "yanked_reason": null
    },
    "last_serial": 12547660,
    "releases": {
        "0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "3d3df6cd4e0b6518ea07feb017eeddda",
                    "sha256": "87d10c9a470c31f3aba44f10d1905e52e0de61fb09d95647678d4800c2b5e374"
                },
                "downloads": -1,
                "filename": "pyreference-0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "3d3df6cd4e0b6518ea07feb017eeddda",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 12905,
                "upload_time": "2018-01-24T06:09:05",
                "upload_time_iso_8601": "2018-01-24T06:09:05.363162Z",
                "url": "https://files.pythonhosted.org/packages/5b/07/0aece74fb17241220b180b0f0c2b81311ccb4c4a8595b0f1cec258573365/pyreference-0.1.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ],
        "0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "9b1acc379e3da070ecf161bf273ffe4e",
                    "sha256": "4bd31d521e0ccc9bab927944e5514b9a095f50f4464391591aab7449e516755b"
                },
                "downloads": -1,
                "filename": "pyreference-0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "9b1acc379e3da070ecf161bf273ffe4e",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 13660,
                "upload_time": "2018-01-25T06:09:56",
                "upload_time_iso_8601": "2018-01-25T06:09:56.132960Z",
                "url": "https://files.pythonhosted.org/packages/ad/d1/ee3c548d96b8e9268897a98962ce4f41c61593c48a8c5ce5574fdd043ac7/pyreference-0.2.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ],
        "0.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0038aece354905f57e89f7a9df7d0464",
                    "sha256": "a8ad3bb31995cdad832fe26f30ae27f908ca1310521f84b229499722218ce00b"
                },
                "downloads": -1,
                "filename": "pyreference-0.3.tar.gz",
                "has_sig": false,
                "md5_digest": "0038aece354905f57e89f7a9df7d0464",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*",
                "size": 14043,
                "upload_time": "2018-06-26T07:54:59",
                "upload_time_iso_8601": "2018-06-26T07:54:59.070655Z",
                "url": "https://files.pythonhosted.org/packages/8a/80/bc4588a7aa8d5d9e3341794147616aa5cbaf2cd837dd6d33c86b5105b91c/pyreference-0.3.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ],
        "0.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "605b1f81b7ac54ed76ea7ea0398e3602",
                    "sha256": "e165b8ec4b1ff1aa359a017dbc07255247380e67c80d79a463238e7f3c9205ed"
                },
                "downloads": -1,
                "filename": "pyreference-0.4.tar.gz",
                "has_sig": false,
                "md5_digest": "605b1f81b7ac54ed76ea7ea0398e3602",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*",
                "size": 14877,
                "upload_time": "2019-10-31T05:07:06",
                "upload_time_iso_8601": "2019-10-31T05:07:06.989253Z",
                "url": "https://files.pythonhosted.org/packages/e7/2a/bfa2d401fb7110ef307ca4b645fdbd8bb6fa30fa7f1a1b1cf46063492a96/pyreference-0.4.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ],
        "0.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b88e8257813e2bd6b0af432b5ca2b045",
                    "sha256": "a5ef17f11f70aa8add1d5bb85f9908c70d8544919fd27cae0d0d85bf92e0f7ec"
                },
                "downloads": -1,
                "filename": "pyreference-0.5-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "b88e8257813e2bd6b0af432b5ca2b045",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=2.7, >=3.5",
                "size": 19282,
                "upload_time": "2020-02-24T02:39:37",
                "upload_time_iso_8601": "2020-02-24T02:39:37.902141Z",
                "url": "https://files.pythonhosted.org/packages/46/f0/22d0496ba5d5f102a17f9c01855f1af93ae3befd7e4427e6fa3b6cf42015/pyreference-0.5-py3-none-any.whl",
                "yanked": false,
                "yanked_reason": null
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "b17987ac0386ffa4976e3244be72d8ce",
                    "sha256": "e8bc0a8016bb2957538df82c742c7e2c7393f8475a06496f91c0b859cc358c2f"
                },
                "downloads": -1,
                "filename": "pyreference-0.5.tar.gz",
                "has_sig": false,
                "md5_digest": "b17987ac0386ffa4976e3244be72d8ce",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=2.7, >=3.5",
                "size": 14934,
                "upload_time": "2020-02-24T02:39:39",
                "upload_time_iso_8601": "2020-02-24T02:39:39.847350Z",
                "url": "https://files.pythonhosted.org/packages/95/ae/6a13ab553f4e603f3a1fdc065c18ed7578256afa02cc0d420dbdd731cd01/pyreference-0.5.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ],
        "0.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0061b817b96b38516e88ce1a95f07529",
                    "sha256": "7cc899b8470b7f317aeb4b9d4a4971b5f23afa8ff0c4b1ba99ace5342694a36c"
                },
                "downloads": -1,
                "filename": "pyreference-0.6-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "0061b817b96b38516e88ce1a95f07529",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=2.7, >=3.5",
                "size": 22702,
                "upload_time": "2021-11-05T04:32:41",
                "upload_time_iso_8601": "2021-11-05T04:32:41.907552Z",
                "url": "https://files.pythonhosted.org/packages/9a/de/4c54dc6a54bf0fdf958c2103053d8975bfa851f5abbc8a686ecccdb7eb75/pyreference-0.6-py3-none-any.whl",
                "yanked": false,
                "yanked_reason": null
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "0b574e5fccbc03fcffbd66e9ec4492e0",
                    "sha256": "4c40abfe7d68128c1e120ad88f9aa656cbee995cd9be4562a4039bd150adba50"
                },
                "downloads": -1,
                "filename": "pyreference-0.6.tar.gz",
                "has_sig": false,
                "md5_digest": "0b574e5fccbc03fcffbd66e9ec4492e0",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=2.7, >=3.5",
                "size": 18890,
                "upload_time": "2021-11-05T04:32:43",
                "upload_time_iso_8601": "2021-11-05T04:32:43.263088Z",
                "url": "https://files.pythonhosted.org/packages/da/89/dee8af2c8316b05c241741b58a2e0048d9614c594bcfab6106567e4ca9ca/pyreference-0.6.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ],
        "0.6.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "27c405fd3598152b2afe632008c7e5d4",
                    "sha256": "8bfd0c3316ea193c1a8470d4f3b51be6cb8b0ac7712b66a89653a47cce9a5bd1"
                },
                "downloads": -1,
                "filename": "pyreference-0.6.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "27c405fd3598152b2afe632008c7e5d4",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=2.7, >=3.5",
                "size": 27730,
                "upload_time": "2022-01-12T03:38:33",
                "upload_time_iso_8601": "2022-01-12T03:38:33.610812Z",
                "url": "https://files.pythonhosted.org/packages/29/4c/07f27226f6f943bf8cc6fc0bbb78b8919364ad1bfc40c84c60c5052d3e11/pyreference-0.6.2-py3-none-any.whl",
                "yanked": false,
                "yanked_reason": null
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "cdd258ff33ad0f45943b74d3129fc43f",
                    "sha256": "e3da2f8c20b45fc40325c04e06b3a5d15d83c078dbb372ed1f664f9fb8b4f972"
                },
                "downloads": -1,
                "filename": "pyreference-0.6.2.tar.gz",
                "has_sig": false,
                "md5_digest": "cdd258ff33ad0f45943b74d3129fc43f",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=2.7, >=3.5",
                "size": 23895,
                "upload_time": "2022-01-12T03:38:35",
                "upload_time_iso_8601": "2022-01-12T03:38:35.343319Z",
                "url": "https://files.pythonhosted.org/packages/90/77/7b9ac70138c7beb9d723240dc86b204f0f1aec798ba270909ec1d0194cd2/pyreference-0.6.2.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ],
        "0.6.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "dda0720fb5fd3706b808453d7bf15ca9",
                    "sha256": "830c5845061b7075ec2507925153dec76a5c1d264d5828fccacd0003fabd9f2c"
                },
                "downloads": -1,
                "filename": "pyreference-0.6.3-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "dda0720fb5fd3706b808453d7bf15ca9",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=2.7, >=3.5",
                "size": 27861,
                "upload_time": "2022-01-12T05:29:31",
                "upload_time_iso_8601": "2022-01-12T05:29:31.947002Z",
                "url": "https://files.pythonhosted.org/packages/fa/ba/da6e73b299b502c7a6aff99044aaf7247ab81dda77293edd6ad2d57c8cbb/pyreference-0.6.3-py3-none-any.whl",
                "yanked": false,
                "yanked_reason": null
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "4c7090961f609850352cd350e5259266",
                    "sha256": "58a2d9f84936d5c77b3b71db0d6a96bc16d39cf56a9f1d32830a9453d6d0d8fc"
                },
                "downloads": -1,
                "filename": "pyreference-0.6.3.tar.gz",
                "has_sig": false,
                "md5_digest": "4c7090961f609850352cd350e5259266",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=2.7, >=3.5",
                "size": 23996,
                "upload_time": "2022-01-12T05:29:33",
                "upload_time_iso_8601": "2022-01-12T05:29:33.792406Z",
                "url": "https://files.pythonhosted.org/packages/c3/77/3931d8ed1e7d2a88563c22273c83a16ed2f2ce957c079715cf80f316b302/pyreference-0.6.3.tar.gz",
                "yanked": false,
                "yanked_reason": null
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "dda0720fb5fd3706b808453d7bf15ca9",
                "sha256": "830c5845061b7075ec2507925153dec76a5c1d264d5828fccacd0003fabd9f2c"
            },
            "downloads": -1,
            "filename": "pyreference-0.6.3-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "dda0720fb5fd3706b808453d7bf15ca9",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=2.7, >=3.5",
            "size": 27861,
            "upload_time": "2022-01-12T05:29:31",
            "upload_time_iso_8601": "2022-01-12T05:29:31.947002Z",
            "url": "https://files.pythonhosted.org/packages/fa/ba/da6e73b299b502c7a6aff99044aaf7247ab81dda77293edd6ad2d57c8cbb/pyreference-0.6.3-py3-none-any.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "4c7090961f609850352cd350e5259266",
                "sha256": "58a2d9f84936d5c77b3b71db0d6a96bc16d39cf56a9f1d32830a9453d6d0d8fc"
            },
            "downloads": -1,
            "filename": "pyreference-0.6.3.tar.gz",
            "has_sig": false,
            "md5_digest": "4c7090961f609850352cd350e5259266",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=2.7, >=3.5",
            "size": 23996,
            "upload_time": "2022-01-12T05:29:33",
            "upload_time_iso_8601": "2022-01-12T05:29:33.792406Z",
            "url": "https://files.pythonhosted.org/packages/c3/77/3931d8ed1e7d2a88563c22273c83a16ed2f2ce957c079715cf80f316b302/pyreference-0.6.3.tar.gz",
            "yanked": false,
            "yanked_reason": null
        }
    ],
    "vulnerabilities": []
}