Metadata-Version: 2.1
Name: bgvep
Version: 0.3
Summary: BBGLab tool
Home-page: https://bitbucket.org/bgframework/bgvep
Author: Barcelona Biomedical Genomics Lab
Author-email: bbglab@irbbarcelona.org
License: Apache Software License 2.0
Description: 
        BGVEP
        =====
        
        Read data generated within the **bgvep** project.
        Within that project there are two datasets, both identified by
        the reference genome (e.g. hg19) and the VEP version (e.g. 88):
        
        - a tabix file with the run of vep for all positions in the genome
        - a bgpack file with only the most severe consequence type.
        
        
        Installation
        ------------
        
        This project is a Python package
        and can be installed with ``pip``.
        Download the source code, get into this
        project directory and execute:
        
        .. code:: bash
        
           pip install .
        
        
        Usage
        -----
        
        To request the output of 1 or more positions, simply indicate the
        chromosome, the initial and the final positions you are interested.
        
        
        
        Commad line usage
        *****************
        
        Execute :code:`bgvep --help` for getting all the information.
        
        The output is printed to the screen using tabs as separators for the indexes:
        
        .. code:: bash
        
           bgvep --genome hg19 --vep 88 --chromosome chr1 --begin 100000 --end 100004
        
        
        Adding the ``--most-severe`` flags, returns the most severe consequence type
        for the 3 possible changes of the allele in that position.
        
        
        
        Python usage
        ************
        
        The easiest way to use **bgvep** is to make use of the generators **get** and
        **get_most_severe**.
        
        .. code:: python
        
           from bgvep import get
           for data in get('hg19', '88', 'chr1', 100000, 100004):
               ...
        
        However, the *best* way to use **bgvep** is using directly the readers:
        the *Tabix* and the *BGPack* readers, which are context managers.
        
        .. code:: python
        
           from bgvep.readers import Tabix
        
           with Tabix('hg19', '88') as reader:
                for data in reader.get('chr1', 100000, 100004):
                     ...
        
        
        The advantage of using directly the readers is that they are not instantiated
        on every call.
        
        
        The output
        ----------
        
        
        The format of the output is:
        
        - Chromosome
        - Position
        - Reference
        - Alternate
        - Gene
        - Feature
        - Feature_type
        - Consequence
        - cDNA_position
        - CDS_position
        - Protein_position
        - Amino_acids
        - Codons
        - Existing_variation
        - Impact
        - Distance
        - Strand
        - Flags
        - Symbol
        - Symbol source
        - HGNC_ID
        - Canonical
        - ENSP
        
        
        When asking for the **most-severe** consquence type, the output is formed
        by the most severe consequente type of all the possible changes of the reference
        allele. The order is always ACGT, and if the refernce allele changes to itself,
        nothing is returned for it.
        
        
        Support
        -------
        
        If you are having issues, please let us know.
        You can contact us at: bbglab@irbbarcelona.org
        
Platform: UNKNOWN
Description-Content-Type: text/x-rst
