.. automodule:: obiuniq


   
   :py:mod:`obiuniq` specific options
   ------------------------------------   

   .. cmdoption::  -m <KEY>, --merge=<KEY>   

        Attribute to merge

    *Example:*
    
            .. code-block:: bash
    
                > obiuniq -m sample seq1.fasta > seq2.fasta
        
        Dereplicates sequences and keep track of samples of origin

   .. cmdoption::  -i , --merge-ids',
       
        Add a ``merged`` attribute containing the list of sequence record ids merged
        within this group
   
   .. cmdoption::  -c <KEY>, --category-attribute=<KEY>

        Add one attribute to the list of attributes used to group sequences before
        dereplication (option can be used several times)

    *Example:*
    
            .. code-block:: bash
    
                > obiuniq -c sample seq1.fasta > seq2.fasta
        
        Dereplicates sequences within each sample

   .. cmdoption::  -p','--prefix',
        
        Dereplication is done based on prefix matching:
        
        1. The shortest sequence of each group is a prefix of any sequence of its group
        2. The shortest sequence of a group is the prefix of only the sequence belonging
           to its group 


   .. include:: ../optionsSet/taxonomyDB.txt

   .. include:: ../optionsSet/inputformat.txt

   .. include:: ../optionsSet/defaultoptions.txt
