{ "info": { "author": "Luca Cappelletti", "author_email": "cappelletti.luca94@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3" ], "description": "pybwtool\n=========================================================================================\n|travis| |sonar_quality| |sonar_maintainability| |codacy|\n|code_climate_maintainability| |pip| |downloads|\n\nPython wrapper for the `bwtool library `_.\nPlease take a look to the `bwtool wiki `_ for notes\non the installation process and to the known issues \nlisted below within this readme.\n\nHow do I install this package?\n----------------------------------------------\nAs usual, just download it using pip:\n\n.. code:: shell\n\n pip install pybwtool\n\nTests Coverage\n----------------------------------------------\nSince some software handling coverages sometimes get slightly\ndifferent results, here's three of them:\n\n|coveralls| |sonar_coverage| |code_climate_coverage|\n\nExtract\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nThe :code:`extract` method returns a tuple of pandas Dataframes\nwith the data from the regions of a bed file extracted from the given bigwig.\n\n.. code:: python\n\n from pybwtool import extract\n\n results = extract(\n bed_path=\"path/to/my/bed_file.bed\",\n bigwig_path=\"path/to/my/bigwig_file.bigwig\"\n )\n\nYou can also run the extraction directly to a file,\na thing that can get handy when you have to run\na very big bed file. You just need to specify a target file.\n\n.. code:: python\n\n from pybwtool import extract\n\n extract(\n bed_path=\"path/to/my/bed_file.bed\",\n bigwig_path=\"path/to/my/bigwig_file.bigwig\",\n target=\"target.bed\"\n )\n\nIt is also possible to directly export\nto a compressed file just by adding the\ngzip extension, as follows:\n\n.. code:: python\n\n from pybwtool import extract\n\n extract(\n bed_path=\"path/to/my/bed_file.bed\",\n bigwig_path=\"path/to/my/bigwig_file.bigwig\",\n target=\"target.bed.gz\"\n )\n\nCommon fixes for getting bwtool to work\n----------------------------------------------\nConsider looking at the Travis-CI configuration.\nIf it works there, it should also work for you.\n\n- `For when the installation of bwtool gets stuck `_\n- `For when the installation of libbeato (a required library) gets stuck `_\n\n\n\n.. |travis| image:: https://travis-ci.org/LucaCappelletti94/pybwtool.png\n :target: https://travis-ci.org/LucaCappelletti94/pybwtool\n :alt: Travis CI build\n\n.. |sonar_quality| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_pybwtool&metric=alert_status\n :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_pybwtool\n :alt: SonarCloud Quality\n\n.. |sonar_maintainability| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_pybwtool&metric=sqale_rating\n :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_pybwtool\n :alt: SonarCloud Maintainability\n\n.. |sonar_coverage| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_pybwtool&metric=coverage\n :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_pybwtool\n :alt: SonarCloud Coverage\n\n.. |coveralls| image:: https://coveralls.io/repos/github/LucaCappelletti94/pybwtool/badge.svg?branch=master\n :target: https://coveralls.io/github/LucaCappelletti94/pybwtool?branch=master\n :alt: Coveralls Coverage\n\n.. |pip| image:: https://badge.fury.io/py/pybwtool.svg\n :target: https://badge.fury.io/py/pybwtool\n :alt: Pypi project\n\n.. |downloads| image:: https://pepy.tech/badge/pybwtool\n :target: https://pepy.tech/badge/pybwtool\n :alt: Pypi total project downloads \n\n.. |codacy| image:: https://api.codacy.com/project/badge/Grade/6f79fce7cb144f509ed584af3f950ab8\n :target: https://www.codacy.com/manual/LucaCappelletti94/pybwtool?utm_source=github.com&utm_medium=referral&utm_content=LucaCappelletti94/pybwtool&utm_campaign=Badge_Grade\n :alt: Codacy Maintainability\n\n.. |code_climate_maintainability| image:: https://api.codeclimate.com/v1/badges/68b5e35660142727406a/maintainability\n :target: https://codeclimate.com/github/LucaCappelletti94/pybwtool/maintainability\n :alt: Maintainability\n\n.. |code_climate_coverage| image:: https://api.codeclimate.com/v1/badges/68b5e35660142727406a/test_coverage\n :target: https://codeclimate.com/github/LucaCappelletti94/pybwtool/test_coverage\n :alt: Code Climate Coverate", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/LucaCappelletti94/pybwtool", "keywords": "", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "pybwtool", "package_url": "https://pypi.org/project/pybwtool/", "platform": "", "project_url": "https://pypi.org/project/pybwtool/", "project_urls": { "Homepage": "https://github.com/LucaCappelletti94/pybwtool" }, "release_url": "https://pypi.org/project/pybwtool/1.0.8/", "requires_dist": null, "requires_python": "", "summary": "Python wrapper for the bwtool library.", "version": "1.0.8", "yanked": false, "yanked_reason": null }, "last_serial": 6767754, "releases": { "1.0.0": [ { "comment_text": "", "digests": { "md5": "74bd1e9aa6e72c9ce3f5679860905430", "sha256": "969f201ecfd31cb2066dc446632debbb91601e76f5140e830f01de688944fd5e" }, "downloads": -1, "filename": "pybwtool-1.0.0.tar.gz", "has_sig": false, "md5_digest": "74bd1e9aa6e72c9ce3f5679860905430", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 3843, "upload_time": "2019-10-25T12:55:43", "upload_time_iso_8601": "2019-10-25T12:55:43.848575Z", "url": "https://files.pythonhosted.org/packages/43/e8/e77f637a3ffd07a229d90c71b117fcce48e9a5409e99316aa878262a75d2/pybwtool-1.0.0.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.1": [ { "comment_text": "", "digests": { "md5": "5111d2c65ca8c99f80317c1af5ecc678", "sha256": "e09ffffc1830df4e06491c46f1f04431e960dd6834557e6441201705a086ab28" }, "downloads": -1, "filename": "pybwtool-1.0.1.tar.gz", "has_sig": false, "md5_digest": "5111d2c65ca8c99f80317c1af5ecc678", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 3929, "upload_time": "2019-11-07T14:19:19", "upload_time_iso_8601": "2019-11-07T14:19:19.787948Z", "url": "https://files.pythonhosted.org/packages/1e/71/2636272710dad01f4946aaa27868b28ebe1e69b31ccbc55cf5e4a47d0b52/pybwtool-1.0.1.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.2": [ { "comment_text": "", "digests": { "md5": "09a3b982d896ed8bb891da9cf3e9af0d", "sha256": "01ba404c580e5dbabeb4ac8991d24f7fa4bc53f65ed54f3ef95a7adab6158aa0" }, "downloads": -1, "filename": "pybwtool-1.0.2.tar.gz", "has_sig": false, "md5_digest": "09a3b982d896ed8bb891da9cf3e9af0d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8044, "upload_time": "2020-02-07T09:34:42", "upload_time_iso_8601": "2020-02-07T09:34:42.169316Z", "url": "https://files.pythonhosted.org/packages/c9/fc/28f797c154967deb0654d07dd1661396a5231f91cd96ad5e9ae7e2aa5ef8/pybwtool-1.0.2.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.3": [ { "comment_text": "", "digests": { "md5": "18b1dbae94e12170c5093e0cd6845099", "sha256": "ad8df3ab79ffe6ce67272edc9f8e26f58032dc4af535733930b3a0253aa4b3b6" }, "downloads": -1, "filename": "pybwtool-1.0.3.tar.gz", "has_sig": false, "md5_digest": "18b1dbae94e12170c5093e0cd6845099", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9386, "upload_time": "2020-02-07T11:43:55", "upload_time_iso_8601": "2020-02-07T11:43:55.915115Z", "url": "https://files.pythonhosted.org/packages/6c/43/aadc2f4a4ceb9152c5f2187c636a23e6a6b3fb2ed08d1452a8fbeb86bff3/pybwtool-1.0.3.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.4": [ { "comment_text": "", "digests": { "md5": "b8a69121ecdc17cd2122dbe981200aba", "sha256": "ba677d60ad71cf531e645166b32c3bbe46a9dd569a253f59cc3e948841dc4b08" }, "downloads": -1, "filename": "pybwtool-1.0.4.tar.gz", "has_sig": false, "md5_digest": "b8a69121ecdc17cd2122dbe981200aba", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9794, "upload_time": "2020-03-06T21:02:51", "upload_time_iso_8601": "2020-03-06T21:02:51.567846Z", "url": "https://files.pythonhosted.org/packages/48/b1/ff121c9fae30283ec3dd6bb8f3a4829327cbdcc4e27f0bb8b08dfa26cc57/pybwtool-1.0.4.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.5": [ { "comment_text": "", "digests": { "md5": "5d50cb07a7e7dbb5ed169ee6984b29a2", "sha256": "136dbae12d646055e4819bbf85b14ed1294b3636112a15d29876fc63bf2378f6" }, "downloads": -1, "filename": "pybwtool-1.0.5.tar.gz", "has_sig": false, "md5_digest": "5d50cb07a7e7dbb5ed169ee6984b29a2", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9802, "upload_time": "2020-03-06T22:13:06", "upload_time_iso_8601": "2020-03-06T22:13:06.248546Z", "url": "https://files.pythonhosted.org/packages/37/00/0efb43e2363a4ef787745984a54a953916a7b6b81856ae62b9b468fcd9c8/pybwtool-1.0.5.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.6": [ { "comment_text": "", "digests": { "md5": "02fe343ec0bd8b16c81ee59f9477856b", "sha256": "e80ea243ffb407b7bc5d72a71db26c5d258aec8b76d1b3c38ee6591bfb9d1a36" }, "downloads": -1, "filename": "pybwtool-1.0.6.tar.gz", "has_sig": false, "md5_digest": "02fe343ec0bd8b16c81ee59f9477856b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9803, "upload_time": "2020-03-06T22:24:19", "upload_time_iso_8601": "2020-03-06T22:24:19.246787Z", "url": "https://files.pythonhosted.org/packages/ef/de/891f6ce86afc56e415d50092d357dd52b744f633927a279bbd5ef059d406/pybwtool-1.0.6.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.7": [ { "comment_text": "", "digests": { "md5": "f9d523b4608d8a3545ce56ecc5cd4555", "sha256": "872f0f2fd2e35fb94cd560af885ed5872fe7df692646a75125cc109433f27610" }, "downloads": -1, "filename": "pybwtool-1.0.7.tar.gz", "has_sig": false, "md5_digest": "f9d523b4608d8a3545ce56ecc5cd4555", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9790, "upload_time": "2020-03-06T22:44:18", "upload_time_iso_8601": "2020-03-06T22:44:18.848711Z", "url": "https://files.pythonhosted.org/packages/5b/19/5df66db79d83b1baf392ce0ea85fbb2051e633f024e2292a8e3bfc67def2/pybwtool-1.0.7.tar.gz", "yanked": false, "yanked_reason": null } ], "1.0.8": [ { "comment_text": "", "digests": { "md5": "b51b930cd17ff0051e02c424052488ee", "sha256": "8cf342e645f7809cb2a4415818c57e731d8a360e3e6caa389c2665fa928853a2" }, "downloads": -1, "filename": "pybwtool-1.0.8.tar.gz", "has_sig": false, "md5_digest": "b51b930cd17ff0051e02c424052488ee", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4947, "upload_time": "2020-03-07T12:46:26", "upload_time_iso_8601": "2020-03-07T12:46:26.615121Z", "url": "https://files.pythonhosted.org/packages/3d/a4/40686f9b7620eaf277a65884a16d90b70474df01742993cc8675ca6a2783/pybwtool-1.0.8.tar.gz", "yanked": false, "yanked_reason": null } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "b51b930cd17ff0051e02c424052488ee", "sha256": "8cf342e645f7809cb2a4415818c57e731d8a360e3e6caa389c2665fa928853a2" }, "downloads": -1, "filename": "pybwtool-1.0.8.tar.gz", "has_sig": false, "md5_digest": "b51b930cd17ff0051e02c424052488ee", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4947, "upload_time": "2020-03-07T12:46:26", "upload_time_iso_8601": "2020-03-07T12:46:26.615121Z", "url": "https://files.pythonhosted.org/packages/3d/a4/40686f9b7620eaf277a65884a16d90b70474df01742993cc8675ca6a2783/pybwtool-1.0.8.tar.gz", "yanked": false, "yanked_reason": null } ], "vulnerabilities": [] }