{ "info": { "author": "Yuanhua Huang", "author_email": "yuanhua@ebi.ac.uk", "bugtrack_url": null, "classifiers": [], "description": "BRIE-kit\n========\n\nPreprocessing tool kit of BRIE project in splicing analysis\n\nWhy BRIE-kit\n------------\n\nThe purpose of move some utility functions from BRIE_ main package into this \ntool kit is that ``brie-event`` is only supported by Python 2 (see issue_). \nTherefore, we keep a few pre-processing tools into this package and BRIE main \npackage can focus on splicing quantification and downstream analysis. \n\n**Therefore, use BRIE-kit in Python 2 environment only for full fucntions.**\n\n.. _BRIE: https://github.com/huangyh09/brie\n.. _issue: https://github.com/huangyh09/brie/issues/12\n\nSupported fucntions\n-------------------\n\nBRIE-kit provides following functions through command line, which are upgraded\nfrom BRIE main package:\n\n1. ``briekit-event``: Extract the splicing events from gene annotation file in \ngff3/gtf formate.\n\n2. ``briekit-event-filter``: Filter exon-skipping events by setting \nthresholds.\n\n3. ``briekit-factor``: Fetch genentic features from genome sequence reference \nfile in fasta formate.\n\n\nQuick Start\n-----------\n\n**Installation** \n\nBRIE-kit is developed under Python 2.7 environment, and not full compatible \nwith Python 3, **so please use it in Python2 environment**. If you are using\nPython3 in Anaconda_ 3, you can simply create a conda_ environment with \nPython=2.7:\n\n.. code-block:: bash\n\n conda create -n briekit python=2.7 numpy=1.13.0 \n\n source activate briekit\n\nOnce you are in a Python 2 environment, there are two ways to isntall: \n\n- Opt 1: Type in terminal: ``pip install briekit``. Add ``-U`` if you want to \n upgrade your earlier installation.\n- Opt 2: Download the GitHub repository_, and type ``python setup.py install``\n\nNote, if you don't use Anaconda_ and don't have root permission, add \n``--user``, so you can install it in your folder.\n\n.. _conda: https://conda.io/docs/user-guide/tasks/manage-environments.html\n.. _Anaconda: https://anaconda.org\n.. _repository: https://github.com/huangyh09/briekit\n\n\n**Arguments**\n\n- Type command line ``briekit-event -h``\n\n\nDetailed manual\n---------------\n\nSee the Wiki_ documentation on how to install, to use, to find the annotation data \netc.\n\n.. _Wiki: https://github.com/huangyh09/briekit/wiki\n\n\nReferences\n----------\n\nYuanhua Huang and Guido Sanguinetti. `BRIE: transcriptome-wide splicing \nquantification in single cells\n`_. \n\\ **Genome Biology**\\, 2017; 18(1):123.", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/huangyh09/briekit", "keywords": "Splicing events annotation,Sequence features", "license": "Apache-2.0", "maintainer": "", "maintainer_email": "", "name": "briekit", "package_url": "https://pypi.org/project/briekit/", "platform": "", "project_url": "https://pypi.org/project/briekit/", "project_urls": { "Homepage": "https://github.com/huangyh09/briekit" }, "release_url": "https://pypi.org/project/briekit/0.2.2/", "requires_dist": null, "requires_python": "", "summary": "BRIE-kit: Preprocessing tool kit of BRIE in splicing analysis", "version": "0.2.2" }, "last_serial": 3925152, "releases": { "0.2.0": [ { "comment_text": "", "digests": { "md5": "4a87281b6fa428105aeee642725ac701", "sha256": "511227757af4a37b009ed51de712f02c5f92cba00311cdce00c3ffc187f33043" }, "downloads": -1, "filename": "briekit-0.2.0.tar.gz", "has_sig": false, "md5_digest": "4a87281b6fa428105aeee642725ac701", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 23103, "upload_time": "2018-05-25T18:16:46", "url": "https://files.pythonhosted.org/packages/4f/36/33d8f4ddcdb3aa40598a592ed112274bc7df4b5e934d6903d5d90320397e/briekit-0.2.0.tar.gz" } ], "0.2.1": [ { "comment_text": "", "digests": { "md5": "f57498b719c6ff3f8f6017194c157acf", "sha256": "a09736757f7b0b624a2e68f1c13ad50d8054836a94b49a328f5e81c6cef95e44" }, "downloads": -1, "filename": "briekit-0.2.1.tar.gz", "has_sig": false, "md5_digest": "f57498b719c6ff3f8f6017194c157acf", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 23236, "upload_time": "2018-05-31T21:55:14", "url": "https://files.pythonhosted.org/packages/d5/9a/348de759069ce591db0b1ee74aa0a63b928f8c81a856824aca4228cd98b7/briekit-0.2.1.tar.gz" } ], "0.2.2": [ { "comment_text": "", "digests": { "md5": "1859f38e47a57f6a371386eeb8fd5662", "sha256": "b710329e4f44bac9549c705fb7471d72e75395f567b7d85e9ed5bd31a884c497" }, "downloads": -1, "filename": "briekit-0.2.2.tar.gz", "has_sig": false, "md5_digest": "1859f38e47a57f6a371386eeb8fd5662", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 41833, "upload_time": "2018-06-03T11:28:44", "url": "https://files.pythonhosted.org/packages/e9/83/a27951cd71ead08d03ff48f10b9cd5f9606e7cb930cd97d9dcd9dd54353e/briekit-0.2.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "1859f38e47a57f6a371386eeb8fd5662", "sha256": "b710329e4f44bac9549c705fb7471d72e75395f567b7d85e9ed5bd31a884c497" }, "downloads": -1, "filename": "briekit-0.2.2.tar.gz", "has_sig": false, "md5_digest": "1859f38e47a57f6a371386eeb8fd5662", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 41833, "upload_time": "2018-06-03T11:28:44", "url": "https://files.pythonhosted.org/packages/e9/83/a27951cd71ead08d03ff48f10b9cd5f9606e7cb930cd97d9dcd9dd54353e/briekit-0.2.2.tar.gz" } ] }