Sequence record editing options
-------------------------------

.. cmdoption::  --seq-rank

                        Adds a new attribute named ``seq_rank`` to the sequence record indicating 
                        its entry number in the sequence file.

                        
.. cmdoption::  -R <OLD_NAME>:<NEW_NAME>, --rename-tag=<OLD_NAME>:<NEW_NAME>

                        Changes attribute name <OLD_NAME> to <NEW_NAME>. When attribute 
                        named <OLD_NAME> is missing, the sequence record is 
                        skipped and the next one is examined.
                        
.. cmdoption::  --delete-tag=<ATTRIBUTE_NAME>

                        Deletes attribute named <ATTRIBUTE_NAME>.When this attribute
                        is missing, the sequence record is skipped and the 
                        next one is examined.
                        
.. cmdoption::  -S <ATTRIBUTE_NAME>:<PYTHON_EXPRESSION>, --set-tag=<ATTRIBUTE_NAME>:<PYTHON_EXPRESSION>

                        Creates a new attribute named <ATTRIBUTE_NAME> with a 
                        value computed from <PYTHON_EXPRESSION>. 
                        
.. cmdoption::  --tag-list=<FILENAME>

                        <FILENAME> points to a file containing attribute 
                        names and values to modify for specified sequence records.
                        
.. cmdoption::  --set-identifier=<PYTHON_EXPRESSION>

                        Sets sequence record identifier with a value computed 
                        from <PYTHON_EXPRESSION>. 

.. cmdoption::  --run=<PYTHON_EXPRESSION>

                        Runs a python expression on each selected sequence.

.. cmdoption::  --set-sequence=<PYTHON_EXPRESSION>

                        Changes the sequence itself with a value computed from 
                        <PYTHON_EXPRESSION>.
                         

.. cmdoption::  -T, --set-definition=<PYTHON_EXPRESSION>

                        Sets sequence definition with a value computed from 
                        <PYTHON_EXPRESSION>.
                        

.. cmdoption::  -O, --only-valid-python

                        Allows only valid python expressions.
                        
.. cmdoption::  -C, --clear

                        Clears all attributes associated to the sequence records.

.. cmdoption::  -k <ATTRIBUTE_NAME>, --keep=<ATTRIBUTE_NAME>

                        Keeps only attribute named <ATTRIBUTE_NAME>. Several ``-k`` 
                        options can be combined.

.. cmdoption::  --length

                        Adds attribute named ``seq_length`` with sequence length as a value.

.. cmdoption::  --with-taxon-at-rank=<RANK_NAME>

                        Adds taxonomic annotation at taxonomic rank 
                        <RANK_NAME>.
                        
.. cmdoption::  -m <MCLFILE>, --mcl=<MCLFILE>

                        Creates a new attribute containing the number of the 
                        cluster the sequence record was assigned to, as 
                        indicated in file <MCLFILE>.

.. cmdoption::  --uniq-id

                        Forces sequence record ids to be unique.
