Metadata-Version: 1.0
Name: CombiVEP
Version: 0.1.0
Summary: Combined Variant Effect Predictors
Home-page: http://pypi.python.org/pypi/combivep/
Author: Jessada Thutkawkorapin
Author-email: jessada115@hotmail.com
License: LICENSE.txt
Description: =============
        Pre-requisite
        =============
        
        * Python 2.7
        * pip (http://pypi.python.org/pypi/pip)
        * numpy (http://pypi.python.org/pypi/numpy)
        * matplotlib (http://matplotlib.org)
        
        ============
        Installation
        ============
        
        To install this module, run the following commands:
        
            sudo python setup.py install
        
        ===========================
        Download reference database
        ===========================
        
        After the installation is complete, type
        
            CombiVEP_reference_updater
        
        This application will automatically check with UCSC and LJB database, and see
        if it is required to download the new one. The original database size is
        around 1GB each. The total operation time for each database should be
        around 30-60 mins.
        
        ========
        Training
        ========
        
        After having reference database installed, the CombiVEP model can be trained
        using
        
            CombiVEP_trainer <training_data_file>
        
        <training_data_file> must be in CBV format: CHROM, POS, REF, ALT,
        ACTUAL_DELETERIOUS_EFFECT. Each field is separated by a tab. SNP Position(POS)
        is 1-based index. The VariBench training data file in CBV format can be found at
        
            combivep/data/CBV/training.cbv
        
        ==========
        Prediction
        ==========
        
        To use the trained model to predict the effect, you can do it using
        
            CombiVEP_predictor <input_file> [-F FORMAT]
        
        The input file can be either in VCF or above CBV format. Default is in
        VCF format. So if you want to use input file in VCF format, simply type
        
            CombiVEP_predictor <vcf_file>
        
        If you to do the prediction using file in CBV format, you can 
        
            CombiVEP_predictor <cbv_file> -F CBV
        
        The VariBench test data file in CBV format can be found at
        
            combivep/data/CBV/test.cbv
        
        
        
        
Platform: UNKNOWN
