{"id":15905976,"url":"https://github.com/lucacappelletti94/pybwtool","last_synced_at":"2025-04-02T22:43:27.623Z","repository":{"id":62579113,"uuid":"217466939","full_name":"LucaCappelletti94/pybwtool","owner":"LucaCappelletti94","description":"Python wrapper for the bwtool library.","archived":false,"fork":false,"pushed_at":"2021-07-16T13:55:34.000Z","size":65465,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-08T21:32:41.026Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LucaCappelletti94.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-10-25T06:33:47.000Z","updated_at":"2021-07-16T13:55:37.000Z","dependencies_parsed_at":"2022-11-03T21:00:21.262Z","dependency_job_id":null,"html_url":"https://github.com/LucaCappelletti94/pybwtool","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpybwtool","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpybwtool/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpybwtool/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpybwtool/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LucaCappelletti94","download_url":"https://codeload.github.com/LucaCappelletti94/pybwtool/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246905830,"owners_count":20852818,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-06T13:20:27.331Z","updated_at":"2025-04-02T22:43:22.605Z","avatar_url":"https://github.com/LucaCappelletti94.png","language":"Python","readme":"pybwtool\n=========================================================================================\n|travis| |sonar_quality| |sonar_maintainability| |codacy|\n|code_climate_maintainability| |pip| |downloads|\n\nPython wrapper for the `bwtool library \u003chttps://github.com/CRG-Barcelona/bwtool\u003e`_.\nPlease take a look to the `bwtool wiki \u003chttps://github.com/CRG-Barcelona/bwtool/wiki#installation\u003e`_ 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 \u003chttps://github.com/CRG-Barcelona/bwtool/issues/65\u003e`_\n- `For when the installation of libbeato (a required library) gets stuck \u003chttps://github.com/CRG-Barcelona/libbeato/issues/6\u003e`_\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\u0026metric=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\u0026metric=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\u0026metric=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\u0026amp;utm_medium=referral\u0026amp;utm_content=LucaCappelletti94/pybwtool\u0026amp;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\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fpybwtool","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flucacappelletti94%2Fpybwtool","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fpybwtool/lists"}