Correspondence
---------------------

Extract event-related genomic alignment.

 
.. rubric:: Parameters

.. tabularcolumns:: column spec

================ ========================================================================
Parameters        Standards and instructions
---------------- ------------------------------------------------------------------------
blockinfo        Type: **file**  |    Default: **-**
                     
                 Output result of parameter `bi`
---------------- ------------------------------------------------------------------------
tandem           Type: **bool**   | Default: **false**

                 Whether to display the collinearity block that may be generated by tandem.
---------------- ------------------------------------------------------------------------
tandem_length    Type: **int**   | Default: **200**

                 If tandem=true, the maximum range of tandem influence.
---------------- ------------------------------------------------------------------------
pvalue            Type: **float**  |    Default: **1**

                  Evaluate the compactness and uniqueness of collinear blocks, the range is 0-1, the better collinearity range is 0-0.2.
---------------- ------------------------------------------------------------------------ 
block_length     Type: **int**   |   Default: **5**
                     
                 Show the minimum length of a collinear block.
---------------- ------------------------------------------------------------------------
multiple         Type: **int**   |    Default: **1**

                 The best number of homologous genes shown with red dots.
---------------- ------------------------------------------------------------------------ 
homo             Type: **int [1-5]**   Default: **1**

                 Evaluate the ratio of the best homologous gene pairs of collinearity block, with a range of -1, 1.
---------------- ------------------------------------------------------------------------
savefile         Type: **file**   |  Default: \* **.csv**
                    
                 The resulting file.
================ ========================================================================

Use command to enter the folder ``wgdi -c ? >> total.conf`` Take out the parameter file.

.. code-block:: python

    [correspondence]
    blockinfo =  blockinfo file(.csv)
    lens1 = lens1 file
    lens2 = lens2 file
    tandem = (true/false)
    tandem_length = 200
    pvalue = 0.2
    block_length = 5
    multiple  = 1
    homo = 0,1
    savefile = savefile(.csv)


.. rubric:: Quick start


The original results are easily accessible at `wgdi-example <https://github.com/SunPengChuan/wgdi-example>`_