Sequence record selection options
---------------------------------

.. cmdoption::  -s <REGULAR_PATTERN>, --sequence=<REGULAR_PATTERN>

                        Regular expression pattern to be tested against the
                        sequence itself. The pattern is case insensitive.

    *Examples:*
    
        .. code-block:: bash
    
                > obigrep -s 'GAATTC' seq1.fasta > seq2.fasta

        Keeps only the sequence records that contain an *EcoRI* restriction site.
    
        .. code-block:: bash
    
                > obigrep -s 'A{10,}' seq1.fasta > seq2.fasta

        Keeps only the sequence records that contain a stretch of at least 10 ``A``.
    
        .. code-block:: bash
    
                > obigrep -s '^[ACGT]+$' seq1.fasta > seq2.fasta

        Keeps only the sequence records that do not contain ambiguous nucleotides.
    

.. cmdoption::  -D <REGULAR_PATTERN>, --definition=<REGULAR_PATTERN>

                        Regular expression pattern to be tested against :doc:`the
                        definition of the sequence record<../fasta>`. The pattern is case
                        sensitive.

    *Example:*
   
        .. code-block:: bash
    
                > obigrep -D '[Cc]hloroplast' seq1.fasta > seq2.fasta
        
        Keeps only the sequence records whose definition contains ``chloroplast`` or
        ``Chloroplast``.
    

.. cmdoption::  -I <REGULAR_PATTERN>, --identifier=<REGULAR_PATTERN>

                        Regular expression pattern to be tested against  :doc:`the
                        identifier of the sequence record <../fasta>`. The pattern is case
                        sensitive.

    *Example:*
   
        .. code-block:: bash
    
                > obigrep -I '^GH' seq1.fasta > seq2.fasta

        Keeps only the sequence records whose identifier begins with ``GH``.
    
  
.. cmdoption::  --id-list=<FILENAME>

                        ``<FILENAME>`` points to a text file containing the list of :doc:`sequence 
                        record identifiers <../fasta>` to be selected. 
                        The file format consists in a single identifier per line.

    *Example:*
       
        .. code-block:: bash
    
               > obigrep --id-list=my_id_list.txt seq1.fasta > seq2.fasta

        Keeps only the sequence records whose identifier is present in the
        ``my_id_list.txt`` file.

.. cmdoption::  -a <ATTRIBUTE_NAME>:<REGULAR_PATTERN>, --attribute=<ATTRIBUTE_NAME>:<REGULAR_PATTERN>

                        Regular expression pattern matched against the
                        :doc:`attributes of the sequence record <../fasta>`. the value of this attribute
                        is of the form : key:regular_pattern. The
                        pattern is case sensitive. Several ``-a`` options can be
                        used on the same command line and in this last case, 
                        the selected sequence records will match all constraints.

    *Example:*
    
        .. code-block:: bash
    
                > obigrep -a 'family_name:Asteraceae' seq1.fasta > seq2.fasta

        Selects the sequence records containing an attribute whose key is ``family_name`` and value
        is ``Asteraceae``.
    
                        
.. cmdoption::  -A <ATTRIBUTE_NAME>, --has-attribute=<KEY>

                        Selects sequence records having an attribute whose key = <KEY>.

    *Example:*
    
        .. code-block:: bash
    
                > obigrep -A taxid seq1.fasta > seq2.fasta

        Keeps only the sequence records having a ``taxid`` attribute defined.
    
                       
.. cmdoption::  -p <PYTHON_EXPRESSION>, --predicat=<PYTHON_EXPRESSION>

                        Python boolean expression to be evaluated for each
                        sequence record. The attribute keys defined for each sequence record
                        can be used in the expression as variable names. 
                        An extra variable named 'sequence' refers to the 
                        sequence record itself.
                        Several -p options can be used on the same command
                        line and in this last case, 
                        the selected sequence records will match all constraints.

    *Example:*
    
        .. code-block:: bash
    
                >  obigrep -p '(forward_error<2) and (reverse_error<2)' seq1.fasta > seq2.fasta

        Keeps only the sequence records whose ``forward_error`` and ``reverse_error``
        attributes have a value smaller than two.
    
                        
.. cmdoption::  -L <##>, --lmax=<##>  

                        Keeps sequence records whose sequence length is 
                        equal or shorter than ``lmax``.
                        
    *Example:*
   
        .. code-block:: bash
    
                > obigrep -L 100 seq1.fasta > seq2.fasta

        Keeps only the sequence records that have a sequence 
        length equal or shorter than 100bp.
    

.. cmdoption::  -l <##>, --lmin=<##>  

                        Keeps sequence records whose sequence length is 
                        equal or longer than ``lmin``.
                        

    *Examples:*
   
        .. code-block:: bash
    
                > obigrep -l 100 seq1.fasta > seq2.fasta

        Keeps only the sequence records that have a sequence length 
        equal or longer than 100bp.
    

.. cmdoption::  -v, --inverse-match   
   
                        Inverts the sequence record selection.

    *Examples:*
   
        .. code-block:: bash
    
                > obigrep -v -l 100 seq1.fasta > seq2.fasta

        Keeps only the sequence records that have a sequence length shorter than 100bp.
    
                        