{ "info": { "author": "", "author_email": "", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License (GPL)", "Programming Language :: Python", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "Overview\n--------\n\n.. image:: https://travis-ci.org/daler/pybedtools.png?branch=master\n :target: https://travis-ci.org/daler/pybedtools\n\n.. image:: https://badge.fury.io/py/pybedtools.svg?style=flat\n :target: http://badge.fury.io/py/pybedtools\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg\n :target: http://bioconda.github.io\n\nThe `BEDTools suite of programs `_ is widely\nused for genomic interval manipulation or \"genome algebra\". `pybedtools` wraps\nand extends BEDTools and offers feature-level manipulations from within\nPython.\n\nSee full online documentation, including installation instructions, at\nhttp://daler.github.io/pybedtools/.\n\nWhy `pybedtools`?\n-----------------\n\nHere is an example to get the names of genes that are <5 kb away from\nintergenic SNPs:\n\n.. code-block:: python\n\n from pybedtools import BedTool\n\n snps = BedTool('snps.bed.gz') # [1]\n genes = BedTool('hg19.gff') # [1]\n\n intergenic_snps = snps.subtract(genes) # [2]\n nearby = genes.closest(intergenic_snps, d=True, stream=True) # [2, 3]\n\n for gene in nearby: # [4]\n if int(gene[-1]) < 5000: # [4]\n print gene.name # [4]\n\nUseful features shown here include:\n\n* `[1]` support for all BEDTools-supported formats (here gzipped BED and GFF)\n* `[2]` wrapping of all BEDTools programs and arguments (here, `subtract` and `closest` and passing\n the `-d` flag to `closest`);\n* `[3]` streaming results (like Unix pipes, here specified by `stream=True`)\n* `[4]` iterating over results while accessing feature data by index or by attribute\n access (here `[-1]` and `.name`).\n\nIn contrast, here is the same analysis using shell scripting. Note that this\nrequires knowledge in Perl, bash, and awk. The run time is identical to the\n`pybedtools` version above:\n\n.. code-block:: bash\n\n snps=snps.bed.gz\n genes=hg19.gff\n intergenic_snps=/tmp/intergenic_snps\n\n snp_fields=`zcat $snps | awk '(NR == 2){print NF; exit;}'`\n gene_fields=9\n distance_field=$(($gene_fields + $snp_fields + 1))\n\n intersectBed -a $snps -b $genes -v > $intergenic_snps\n\n closestBed -a $genes -b $intergenic_snps -d \\\n | awk '($'$distance_field' < 5000){print $9;}' \\\n | perl -ne 'm/[ID|Name|gene_id]=(.*?);/; print \"$1\\n\"'\n\n rm $intergenic_snps\n\nSee the `Shell script comparison `_ in the docs\nfor more details on this comparison, or keep reading the full documentation at\nhttp://daler.github.io/pybedtools.", "description_content_type": "", "docs_url": "https://pythonhosted.org/pybedtools/", "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/daler/pybedtools", "keywords": "", "license": "GPLv2", "maintainer": "Ryan Dale", "maintainer_email": "ryan.dale@nih.gov", "name": "pybedtools", "package_url": "https://pypi.org/project/pybedtools/", "platform": "", "project_url": "https://pypi.org/project/pybedtools/", "project_urls": { "Homepage": "https://github.com/daler/pybedtools" }, "release_url": "https://pypi.org/project/pybedtools/0.8.0/", "requires_dist": null, "requires_python": "", "summary": "Wrapper around BEDTools for bioinformatics work", "version": "0.8.0" }, "last_serial": 4524178, "releases": { "0.2.2dev": [ { "comment_text": "", "digests": { "md5": "0871b88fa2b2d1c83b63de05151cc9ba", "sha256": "6ab084ce36f26c6086680ef25693873f9534ddb3aefec3aedbc8221e5f6f4fb6" }, "downloads": -1, "filename": "pybedtools-0.2.2dev.tar.gz", "has_sig": false, "md5_digest": "0871b88fa2b2d1c83b63de05151cc9ba", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 11674, "upload_time": "2011-01-28T16:39:16", "url": "https://files.pythonhosted.org/packages/00/d9/aca9636b3e5b29f232fd6f60859f07f3420ec3c0712b50cb25c734a02a1f/pybedtools-0.2.2dev.tar.gz" } ], "0.5": [ { "comment_text": "", "digests": { "md5": "3291a68793bcdadeef811b904c0ea1d4", "sha256": "16e46c664e47cd36d926de202d9ac99cf7e8c970e6e008603ccb6a23139a257a" }, "downloads": -1, "filename": "pybedtools-0.5.tar.gz", "has_sig": false, "md5_digest": "3291a68793bcdadeef811b904c0ea1d4", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 17692083, "upload_time": "2011-09-26T19:02:39", "url": "https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz" } ], "0.5.5": [ { "comment_text": "", "digests": { "md5": "7ce2da6ea8f1f31add5b6005cc2ec8ec", "sha256": "4bc9cdadb12fae47c1a2e423f467cfd92dc282a52f2ac5d21c35611ef59c698d" }, "downloads": -1, "filename": "pybedtools-0.5.5.tar.gz", "has_sig": false, "md5_digest": "7ce2da6ea8f1f31add5b6005cc2ec8ec", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 17960588, "upload_time": "2011-11-01T16:00:13", "url": "https://files.pythonhosted.org/packages/e7/9b/f082d2db470a0c9ba777a0d661fd5a7292c367840880040940de4a705e1f/pybedtools-0.5.5.tar.gz" } ], "0.5dev": [ { "comment_text": "", "digests": { "md5": "a207569bccf25ab72ea7ee2467ae7d12", "sha256": "4e55a927a22979473c1414b43154cd3e5a51380b1895bc555a85ee4bf385ba25" }, "downloads": -1, "filename": "pybedtools-0.5dev.tar.gz", "has_sig": false, "md5_digest": "a207569bccf25ab72ea7ee2467ae7d12", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2992172, "upload_time": "2011-06-16T00:36:41", "url": "https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz" } ], "0.5rc1": [ { "comment_text": "", "digests": { "md5": "3dd989c842d6e012845f2c77c555e78a", "sha256": "78ccf10923b00ec14cf337b3b9624e39fdd383ba29048f3cc03e3aabc52edb40" }, "downloads": -1, "filename": "pybedtools-0.5rc1.tar.gz", "has_sig": false, "md5_digest": "3dd989c842d6e012845f2c77c555e78a", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 17688449, "upload_time": "2011-07-12T23:58:27", "url": "https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz" } ], "0.6": [ { "comment_text": "", "digests": { "md5": "85d073faeba199d05907a9c22972fd2d", "sha256": "416406bbf059372e3214c68688447cbb9cd4e45b6a58b1615be4ff932975ede6" }, "downloads": -1, "filename": "pybedtools-0.6.tar.gz", "has_sig": false, "md5_digest": "85d073faeba199d05907a9c22972fd2d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 18123357, "upload_time": "2012-03-13T15:02:44", "url": "https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz" } ], "0.6.1": [ { "comment_text": "", "digests": { "md5": "c67a34e48deb8d747795be09f9bc3dd6", "sha256": "da3f1ec9e6d23cba6627adb124a27d291f72b855006a277d91c1b366bfccdb22" }, "downloads": -1, "filename": "pybedtools-0.6.1.tar.gz", "has_sig": false, "md5_digest": "c67a34e48deb8d747795be09f9bc3dd6", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 17907113, "upload_time": "2012-05-25T23:44:50", "url": "https://files.pythonhosted.org/packages/ac/25/c971ba83c6df08cbd17626339ec637df57a0aa409ba3042408ff349dd710/pybedtools-0.6.1.tar.gz" } ], "0.6.2": [ { "comment_text": "", "digests": { "md5": "ee3677da171973bf4299242efad62685", "sha256": "7263d2a32a4805e0b0c25be32f38a17de760557c2d83234e46364ecd2debec14" }, "downloads": -1, "filename": "pybedtools-0.6.2.tar.gz", "has_sig": false, "md5_digest": "ee3677da171973bf4299242efad62685", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 18129171, "upload_time": "2012-11-05T22:59:36", "url": "https://files.pythonhosted.org/packages/3e/71/cb09c7b874a87803f9fb9a9b679d02a82879b9cadca4c93756e05e65a439/pybedtools-0.6.2.tar.gz" } ], "0.6.3": [ { "comment_text": "", "digests": { "md5": "0d535e3f15a7c1ca00f33261ff366bf3", "sha256": "bd7ad8584d6d19eef175a0f9b9ff00db903db532ae4c3e8bad614246974daff0" }, "downloads": -1, "filename": "pybedtools-0.6.3.tar.gz", "has_sig": false, "md5_digest": "0d535e3f15a7c1ca00f33261ff366bf3", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 18879522, "upload_time": "2013-12-17T00:57:29", "url": "https://files.pythonhosted.org/packages/28/0b/15291a1aac0a2a1eb814a0c883ccebf2eebaebbef9923bfa0444df0cb3a8/pybedtools-0.6.3.tar.gz" } ], "0.6.4": [ { "comment_text": "", "digests": { "md5": "c380fdcc2cefe894728569928d0b18b1", "sha256": "98cd0e8bc278e8d3bf584cde5eea43f23251c91bbd70407172db206d2f3f751f" }, "downloads": -1, "filename": "pybedtools-0.6.4.tar.gz", "has_sig": false, "md5_digest": "c380fdcc2cefe894728569928d0b18b1", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 18980560, "upload_time": "2014-01-08T16:27:36", "url": "https://files.pythonhosted.org/packages/7a/12/73027be04fc57dd3340e2120f0148c0aca569b16e62333f32a40b2b06ee0/pybedtools-0.6.4.tar.gz" } ], "0.6.5": [ { "comment_text": "", "digests": { "md5": "ee1e6f840516fd8105feecf2ac9cb67c", "sha256": "0ee69c4670bae332f6de600af5edb4ed45e8dcaf3988e7eb78ab53a1889a8d9c" }, "downloads": -1, "filename": "pybedtools-0.6.5.tar.gz", "has_sig": false, "md5_digest": "ee1e6f840516fd8105feecf2ac9cb67c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19010017, "upload_time": "2014-04-24T16:08:35", "url": "https://files.pythonhosted.org/packages/a4/98/dab963ff44ddd40849a01b145b6d769158d9794b979fdbfd173728e06e5b/pybedtools-0.6.5.tar.gz" } ], "0.6.6": [ { "comment_text": "", "digests": { "md5": "2fbc9360bb569e3691205aff45b52a01", "sha256": "b7d2436c2f29b92cf7c2a4552a6a13adc73b2026d7a25c4aaae6797589698c68" }, "downloads": -1, "filename": "pybedtools-0.6.6.tar.gz", "has_sig": false, "md5_digest": "2fbc9360bb569e3691205aff45b52a01", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19010568, "upload_time": "2014-05-23T16:54:38", "url": "https://files.pythonhosted.org/packages/a3/91/02e900caea18ee909665440727222a9f37c9a532170c52684123f07d6e21/pybedtools-0.6.6.tar.gz" } ], "0.6.7": [ { "comment_text": "", "digests": { "md5": "786fc6460d04e9c8c8fff7da91055fc5", "sha256": "b31853473db3a755bbe668b5fc209f0cd9ed876f15e192c244e348f4a7cb1cfb" }, "downloads": -1, "filename": "pybedtools-0.6.7.tar.gz", "has_sig": false, "md5_digest": "786fc6460d04e9c8c8fff7da91055fc5", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 42247412, "upload_time": "2014-09-26T02:32:07", "url": "https://files.pythonhosted.org/packages/af/ff/7d488b19b8e4109bbaf7b7e4c5dc53207f2c4354d7729cf73f17a79fa104/pybedtools-0.6.7.tar.gz" } ], "0.6.8": [ { "comment_text": "", "digests": { "md5": "ee1b7a46181d57de3e2d16a656f21aaf", "sha256": "a278a1b5ae230eb9c1b57c4da45dad5646aead899e927ad4d9f38df3f90841db" }, "downloads": -1, "filename": "pybedtools-0.6.8.tar.gz", "has_sig": false, "md5_digest": "ee1b7a46181d57de3e2d16a656f21aaf", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19018059, "upload_time": "2014-11-06T18:10:23", "url": "https://files.pythonhosted.org/packages/aa/e9/c92a7e58326bf76534af1fbd4074def6999130b1838b4dcc51e9f3ba5e17/pybedtools-0.6.8.tar.gz" } ], "0.6.9": [ { "comment_text": "", "digests": { "md5": "b7df049036422d8c6951412a90e83dca", "sha256": "56915b3e2200c6fb56260a36f839e66ce27d7dd3ef55fba278c3931b786fbfd1" }, "downloads": -1, "filename": "pybedtools-0.6.9.tar.gz", "has_sig": false, "md5_digest": "b7df049036422d8c6951412a90e83dca", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 19019805, "upload_time": "2014-12-11T14:19:11", "url": "https://files.pythonhosted.org/packages/79/20/2a0861cc9ffc41043efd814cdf860828f4b2213573c82ea6138eb6cb221b/pybedtools-0.6.9.tar.gz" } ], "0.6rc1": [ { "comment_text": "", "digests": { "md5": "e3f1804fc47881de81be9b0e8eee5012", "sha256": "006e637d2a2e6f98f7b178211adc69fabf3cf37e168c730dbfe9e2fa810f8f8d" }, "downloads": -1, "filename": "pybedtools-0.6rc1.tar.gz", "has_sig": false, "md5_digest": "e3f1804fc47881de81be9b0e8eee5012", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 17968328, "upload_time": "2012-03-06T16:54:03", "url": "https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz" } ], "0.7.0": [ { "comment_text": "", "digests": { "md5": "0434b1d36f3f3415dae26af6a85d88b0", "sha256": "a0b3bd7c32786067a767585ab17ab9e04bf7e227f275ff3883fab9c1d8e458ba" }, "downloads": -1, "filename": "pybedtools-0.7.0.tar.gz", "has_sig": false, "md5_digest": "0434b1d36f3f3415dae26af6a85d88b0", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12564963, "upload_time": "2015-09-03T22:12:31", "url": "https://files.pythonhosted.org/packages/e6/8d/06beb4e8a9e9a4ce042af337a5b855a789da586072d0c418ed9cb9398628/pybedtools-0.7.0.tar.gz" } ], "0.7.1": [ { "comment_text": "", "digests": { "md5": "0b21bf55ba5f97aab387c13be059900f", "sha256": "d889e8e1f75803b13f0f774320ca3e38eea88e7998866a1c90e9ba51caa855be" }, "downloads": -1, "filename": "pybedtools-0.7.1.tar.gz", "has_sig": false, "md5_digest": "0b21bf55ba5f97aab387c13be059900f", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12568915, "upload_time": "2015-09-28T20:49:45", "url": "https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz" } ], "0.7.10": [ { "comment_text": "", "digests": { "md5": "f003c67e22c48b77f070538368ece70c", "sha256": "518a2311bd33f29cf2ee8fc1a028dda8c8e380c9fc83fcb0fbaa206933174b50" }, "downloads": -1, "filename": "pybedtools-0.7.10.tar.gz", "has_sig": false, "md5_digest": "f003c67e22c48b77f070538368ece70c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12601009, "upload_time": "2017-05-31T19:07:44", "url": "https://files.pythonhosted.org/packages/09/57/e7668e8644c60413be05b8cc9c23aaea3a0717b4025843d8c26b7c4822af/pybedtools-0.7.10.tar.gz" } ], "0.7.3": [], "0.7.4": [ { "comment_text": "", "digests": { "md5": "8d49b770b58ea5a348bb1ac19dc31b64", "sha256": "15cfae9e8a207ded403ad9fa2e77f09d14c2fe377d1bc5f8b063647e2d0554e0" }, "downloads": -1, "filename": "pybedtools-0.7.4.tar.gz", "has_sig": false, "md5_digest": "8d49b770b58ea5a348bb1ac19dc31b64", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12576176, "upload_time": "2015-11-25T15:27:20", "url": "https://files.pythonhosted.org/packages/a2/43/d80dbf32da421c78ea84a386402e1840dd06f3aba7e5fe73e8134e1ce50a/pybedtools-0.7.4.tar.gz" } ], "0.7.5": [ { "comment_text": "", "digests": { "md5": "3f150cd4f3ba66c315db3447a847ca37", "sha256": "f2428b4845083eff36385bec241ddddf7488a7de3f18886a78c73226e9e3306c" }, "downloads": -1, "filename": "pybedtools-0.7.5.tar.gz", "has_sig": false, "md5_digest": "3f150cd4f3ba66c315db3447a847ca37", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12578701, "upload_time": "2016-01-25T16:20:33", "url": "https://files.pythonhosted.org/packages/ed/f1/2caa4dc57b62707f0df147c0820d1fc8565e439c5f5c86778df7a2fec59f/pybedtools-0.7.5.tar.gz" } ], "0.7.6": [ { "comment_text": "", "digests": { "md5": "b910c7be9bf26a1508a071e03dfbb7f7", "sha256": "8b6382036c715b49f83e35cc787d7084c1633ebe94a2a3c4102e805613f7426b" }, "downloads": -1, "filename": "pybedtools-0.7.6.tar.gz", "has_sig": false, "md5_digest": "b910c7be9bf26a1508a071e03dfbb7f7", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12586325, "upload_time": "2016-02-01T18:11:25", "url": "https://files.pythonhosted.org/packages/f4/49/ce7ccc0ad79189eb8b8eec170c350643e7a209f98e34dae239a954d6fdb0/pybedtools-0.7.6.tar.gz" } ], "0.7.7": [ { "comment_text": "", "digests": { "md5": "14aa5c7193e20487ec3ff806874f8462", "sha256": "dba8758bd86121e4dcfc8b25ebae7d3b2de6ff9e38e4cdd9dc03f128bf5d4c9d" }, "downloads": -1, "filename": "pybedtools-0.7.7.tar.gz", "has_sig": false, "md5_digest": "14aa5c7193e20487ec3ff806874f8462", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12603926, "upload_time": "2016-03-11T15:38:14", "url": "https://files.pythonhosted.org/packages/c2/a6/29fd41e86b38e7ca39eb7818c422e927534f2bd324c34cfd411cfca203b0/pybedtools-0.7.7.tar.gz" } ], "0.7.8": [ { "comment_text": "", "digests": { "md5": "966d61678f59bba85a3acd3bd48515d5", "sha256": "e80e8b73b233ec6950069e0e1cf14127aff8310a8eaf3ee663bdfbcb61309fdc" }, "downloads": -1, "filename": "pybedtools-0.7.8.tar.gz", "has_sig": false, "md5_digest": "966d61678f59bba85a3acd3bd48515d5", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 14546123, "upload_time": "2016-07-14T01:43:03", "url": "https://files.pythonhosted.org/packages/2d/ee/aa19e50e03e06c817d00eadf8b56824b9e473da8c3e8ca3b33a11717ee6f/pybedtools-0.7.8.tar.gz" } ], "0.7.9": [ { "comment_text": "", "digests": { "md5": "498a9cf0bb6eaf1e6342463da2baa855", "sha256": "e9134d7dc3de41b90126df633fe3aa854a0427d7ada834dc8681081e8b2fea14" }, "downloads": -1, "filename": "pybedtools-0.7.9.tar.gz", "has_sig": false, "md5_digest": "498a9cf0bb6eaf1e6342463da2baa855", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12599296, "upload_time": "2017-01-25T21:33:52", "url": "https://files.pythonhosted.org/packages/7c/66/8aecffd830eddbd05c1c3e737f87220cef9f2a8358f1d692f85b30269520/pybedtools-0.7.9.tar.gz" } ], "0.8.0": [ { "comment_text": "", "digests": { "md5": "3d39cb0a8715d604c04f7a3b68ea81ea", "sha256": "4eebd2cd1764ee1c604fd881703c3e329195485350b987b7fb8db42d232984f6" }, "downloads": -1, "filename": "pybedtools-0.8.0.tar.gz", "has_sig": false, "md5_digest": "3d39cb0a8715d604c04f7a3b68ea81ea", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12496094, "upload_time": "2018-11-24T18:01:53", "url": "https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "3d39cb0a8715d604c04f7a3b68ea81ea", "sha256": "4eebd2cd1764ee1c604fd881703c3e329195485350b987b7fb8db42d232984f6" }, "downloads": -1, "filename": "pybedtools-0.8.0.tar.gz", "has_sig": false, "md5_digest": "3d39cb0a8715d604c04f7a3b68ea81ea", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 12496094, "upload_time": "2018-11-24T18:01:53", "url": "https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz" } ] }