{ "info": { "author": "clintval", "author_email": "valentine.clint@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "

RefGene-Parser

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Installation

\n\nClone the respository and then install locally:\n\n```bash\n$ git clone https://github.com/clintval/refgene-parser.git\n$ pip install refgene-parser\n```\n\n

Dependencies

\n\n- None\n\n

Tutorial

\n\nIterate over the records in a RefGene file:\n\n```python\n\nfrom refgene_parser import RefGene\n\nrefgene = RefGene('mm10.refGene.txt.gz')\n\nfor i, gene in enumerate(refgene):\n if i >= 10: break\n print(gene)\n```\n\n```python\nGene(\"chr2\", 11705292, 11733985, \"+\", name=\"Il15ra\", id=\"NM_001271498\")\nGene(\"chr7\", 142434976, 142440396, \"+\", name=\"Syt8\", id=\"NM_001285857\")\nGene(\"chr1\", 78424744, 78488897, \"-\", name=\"Farsb\", id=\"NM_011811\")\nGene(\"chr11\", 62574485, 62600305, \"+\", name=\"Trpv2\", id=\"NM_011706\")\nGene(\"chr12\", 100199434, 100209824, \"+\", name=\"Calm1\", id=\"NM_009790\")\nGene(\"chr5\", 30933142, 30945480, \"-\", name=\"Cgref1\", id=\"NM_026770\")\nGene(\"chr4\", 142084297, 142088101, \"+\", name=\"Tmem51os1\", id=\"NR_027137\")\nGene(\"chr10\", 77257772, 77259223, \"-\", name=\"Gm10941\", id=\"NR_026944\")\nGene(\"chr10\", 77706586, 77706986, \"+\", name=\"Gm10272\", id=\"NR_026831\")\nGene(\"chr7\", 100549116, 100607996, \"-\", name=\"Mrpl48\", id=\"NR_003559\")\nGene(\"chr7\", 7212995, 7278289, \"-\", name=\"Vmn2r29\", id=\"NR_003555\")\n```\n\n\n
Exact match for a gene symbol name
\n\n> Will return the first record matching with `name == Kras`\n\n```python\nKras = refgene.gene_by_name('Kras')\nprint(Kras)\nprint(Kras.sam_interval)\nprint(Kras.num_exons)\n```\n\n```python\nGene(\"chr6\", 145216698, 145250231, \"-\", name=\"Kras\", id=\"NM_021284\")\n'chr6:145216698-145250231'\n5\n```\n\n\n
Exact match for a gene ID
\n\n> Will return the first record matching `id == NM_009085`\n\n```python\nNM_009085 = refgene.gene_by_id('NM_009085')\n```\n\n```python\nGene(\"chr17\", 46243919, 46248045, \"-\", name=\"Polr1c\", id=\"NM_009085\")\n```\n\n\n
Fuzzy match for a gene symbol name
\n\n```python\nlist(refgene.genes_by_name_pattern('^.ras$'))\n```\n\n```python\n[Gene(\"chr3\", 103058284, 103067914, \"+\", name=\"Nras\", id=\"NM_010937\"),\n Gene(\"chr7\", 45018006, 45021644, \"+\", name=\"Rras\", id=\"NM_009101\"),\n Gene(\"chrX\", 7924275, 7928607, \"-\", name=\"Eras\", id=\"NM_181548\"),\n Gene(\"chr7\", 141189933, 141194004, \"-\", name=\"Hras\", id=\"NM_008284\"),\n Gene(\"chr6\", 145216698, 145250231, \"-\", name=\"Kras\", id=\"NM_021284\"),\n Gene(\"chr9\", 99385419, 99436712, \"-\", name=\"Mras\", id=\"NM_008624\"),\n Gene(\"chr7\", 141189933, 141194004, \"-\", name=\"Hras\", id=\"NM_001130444\"),\n Gene(\"chr7\", 141189933, 141194004, \"-\", name=\"Hras\", id=\"NM_001130443\")]\n```\n\n\n
Fuzzy match for a gene ID
\n\n```python\nlist(refgene.genes_by_id_pattern('NR_00355*'))\n```\n\n```python\n\n[Gene(\"chr7\", 100549116, 100607996, \"-\", name=\"Mrpl48\", id=\"NR_003559\"),\n Gene(\"chr7\", 7212995, 7278289, \"-\", name=\"Vmn2r29\", id=\"NR_003555\"),\n Gene(\"chr15\", 82636749, 82642045, \"-\", name=\"Cyp2d13\", id=\"NR_003552\"),\n Gene(\"chr3\", 92373914, 92375229, \"+\", name=\"Sprr2g\", id=\"NR_003548\"),\n Gene(\"chr13\", 104173720, 104178466, \"-\", name=\"Trappc13\", id=\"NR_003546\"),\n Gene(\"chr5\", 30950065, 30955095, \"+\", name=\"Abhd1\", id=\"NR_003522\"),\n Gene(\"chr17\", 3064317, 3084183, \"-\", name=\"Pisd-ps2\", id=\"NR_003519\"),\n Gene(\"chrUn_JH584304\", 52673, 59689, \"-\", name=\"Pisd-ps3\", id=\"NR_003518\"),\n Gene(\"chr11\", 3124020, 3131944, \"+\", name=\"Pisd-ps1\", id=\"NR_003517\"),\n Gene(\"chr16\", 97536080, 97560901, \"+\", name=\"Mx2\", id=\"NR_003508\"),\n Gene(\"chr5\", 120812634, 120824160, \"+\", name=\"Oas1b\", id=\"NR_003507\"),\n Gene(\"chr5\", 10865028, 10870808, \"+\", name=\"Gm6455\", id=\"NR_003596\"),\n Gene(\"chr19\", 5842295, 5845480, \"-\", name=\"Neat1\", id=\"NR_003513\"),\n Gene(\"chr15\", 62217540, 62219451, \"-\", name=\"H2afy3\", id=\"NR_003523\"),\n Gene(\"chrX_GL456233_random\", 268798, 270075, \"+\", name=\"Zf12\", id=\"NR_003547\"),\n Gene(\"chr16\", 97447034, 97462906, \"-\", name=\"Mx1\", id=\"NR_003520\"),\n Gene(\"chr11\", 88964665, 88966917, \"-\", name=\"Gm15698\", id=\"NR_003564\"),\n Gene(\"chr13\", 12614064, 12650395, \"-\", name=\"Gpr137b-ps\", id=\"NR_003568\")]\n```", "description_content_type": null, "docs_url": null, "download_url": "https://github.com/clintval/refgene-parser/archive/0.0.1.tar.gz", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/clintval/refgene-parser", "keywords": "refgene parser bioinformatics", "license": "MIT License", "maintainer": "", "maintainer_email": "", "name": "refgene_parser", "package_url": "https://pypi.org/project/refgene_parser/", "platform": "", "project_url": "https://pypi.org/project/refgene_parser/", "project_urls": { "Download": "https://github.com/clintval/refgene-parser/archive/0.0.1.tar.gz", "Homepage": "https://github.com/clintval/refgene-parser" }, "release_url": "https://pypi.org/project/refgene_parser/0.0.1/", "requires_dist": null, "requires_python": "", "summary": "Quickly parse genes and exons from a RefGene file", "version": "0.0.1" }, "last_serial": 3223591, "releases": { "0.0.1": [ { "comment_text": "", "digests": { "md5": "8406926c82a5527ff15cd0af92caf1f5", "sha256": "1ef7c7fa146b04d9a54403df5a93f1b0499bab673b6ff888c2aa1a4ed3b69b8b" }, "downloads": -1, "filename": "refgene_parser-0.0.1.tar.gz", "has_sig": false, "md5_digest": "8406926c82a5527ff15cd0af92caf1f5", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4549, "upload_time": "2017-10-03T23:03:20", "url": "https://files.pythonhosted.org/packages/1c/91/07a366e7eca7aedd160a456c6b12a26a987d223700191da062c39c3cceb8/refgene_parser-0.0.1.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "8406926c82a5527ff15cd0af92caf1f5", "sha256": "1ef7c7fa146b04d9a54403df5a93f1b0499bab673b6ff888c2aa1a4ed3b69b8b" }, "downloads": -1, "filename": "refgene_parser-0.0.1.tar.gz", "has_sig": false, "md5_digest": "8406926c82a5527ff15cd0af92caf1f5", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4549, "upload_time": "2017-10-03T23:03:20", "url": "https://files.pythonhosted.org/packages/1c/91/07a366e7eca7aedd160a456c6b12a26a987d223700191da062c39c3cceb8/refgene_parser-0.0.1.tar.gz" } ] }