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.. 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 keeps the value distribution of the ``sample`` attribute
in the new attribute ``merged_sample``.
.. cmdoption:: -i , --merge-ids
Adds a ``merged`` attribute containing the list of sequence record ids merged
within this group.
.. cmdoption:: -c <KEY>, --category-attribute=<KEY>
Adds one attribute to the list of attributes used to define sequence groups
(this 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 sequences belonging
to its group
.. include:: ../optionsSet/taxonomyDB.txt
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`obiuniq` added sequence attributes
-------------------------------------------
.. hlist::
:columns: 3
- :doc:`count <../attributes/count>`
- :doc:`merged_* <../attributes/merged_star>`
- :doc:`merged <../attributes/merged>`
- :doc:`scientific_name <../attributes/scientific_name>`
- :doc:`rank <../attributes/rank>`
- :doc:`family <../attributes/family>`
- :doc:`family_name <../attributes/family_name>`
- :doc:`genus <../attributes/genus>`
- :doc:`genus_name <../attributes/genus_name>`
- :doc:`order <../attributes/order>`
- :doc:`order_name <../attributes/order_name>`
- :doc:`species <../attributes/species>`
- :doc:`species_name <../attributes/species_name>`
:py:mod:`obiuniq` used sequence attribute
-----------------------------------------
- :doc:`taxid <../attributes/taxid>`
|
