Metadata-Version: 1.0
Name: briekit
Version: 0.2.0
Summary: BRIE-kit: Preprocessing tool kit of BRIE in splicing analysis
Home-page: https://github.com/huangyh09/briekit
Author: Yuanhua Huang
Author-email: yuanhua@ebi.ac.uk
License: Apache-2.0
Description: BRIE-kit
        ========
        
        Preprocessing tool kit of BRIE project in splicing analysis
        
        Why BRIE-kit
        ------------
        
        The purpose of move some utility functions from BRIE_ main package into this 
        tool kit is that ``brie-event`` is only supported by Python 2 (see issue_). 
        Therefore, we keep a few pre-processing tools into this package and  BRIE main 
        package can focus on splicing quantification and downstream analysis. 
        
        **Therefore, use BRIE-kit in Python 2 environment only for full fucntions.**
        
        .. _BRIE: https://github.com/huangyh09/brie
        .. _issue: https://github.com/huangyh09/brie/issues/12
        
        Supported fucntions
        -------------------
        
        BRIE-kit provides following functions through command line, which are upgraded
        from BRIE main package:
        
        1. ``briekit-event``: Extract the splicing events from gene annotation file in 
        gff3/gtf formate.
        
        2. ``briekit-event-filter``: Filter exon-skipping events by setting 
        thresholds.
        
        3. ``briekit-factor``: Fetch genentic features from genome sequence reference 
        file in fasta formate.
        
        
        Quick Start
        -----------
        
        **Installation** 
        
        BRIE-kit is developed under Python 2.7 environment, and not full compatible 
        with Python 3, **so please use it in Python2 environment**. If you are using
        Python3 in Anaconda_ 3, you can simply create a conda_ environment with 
        Python=2.7:
        
        .. code-block:: bash
        
          conda create -n briekit python=2.7 numpy=1.13.0 
        
          source activate briekit
        
        Once you are in a Python 2 environment, there are two ways to isntall: 
        
        - Opt 1: Type in terminal: ``pip install briekit``. Add ``-U`` if you want to 
          upgrade your earlier installation.
        - Opt 2: Download the GitHub repository_, and type ``python setup.py install``
        
        Note, if you don't use Anaconda_  and don't have root permission, add 
        ``--user``, so you can install it in your folder.
        
        .. _conda: https://conda.io/docs/user-guide/tasks/manage-environments.html
        .. _Anaconda: https://anaconda.org
        .. _repository: https://github.com/huangyh09/briekit
        
        
        **Arguments**
        
        - Type command line ``briekit-event -h``
        
        
        Detailed manual
        ---------------
        
        See the documentation_ on how to install, to use, to find the annotation data 
        etc.
        
        .. _documentation: https://github.com/huangyh09/briekit/wiki
        
        
        References
        ----------
        
        Yuanhua Huang and Guido Sanguinetti. `BRIE: transcriptome-wide splicing 
        quantification in single cells
        <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1248-5>`_. 
        \ **Genome Biology**\, 2017; 18(1):123.
        
Keywords: Splicing events annotation,Sequence features
Platform: UNKNOWN
