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.. automodule:: obisilva
:py:mod:`obisilva` specific options
-------------------------------------
.. cmdoption:: -s , --ssu
Specify that you are interested in the **SSU** database.
*Example:*
.. code-block:: bash
> obisilva --ssu --parc
This download and format into an ecoPCR database the latest version of the **SSUParc** database of **Silva**.
.. cmdoption:: -l, --lsu
Specify that you are interested in the **LSU** database.
*Example:*
.. code-block:: bash
> obisilva --ssu --parc
This download and format into an ecoPCR database the latest version of the **LSUParc** database of **Silva**.
.. cmdoption:: -p , --parc
Specify that you are interested in the **Parc** (complete) version of the **Silva** database.
.. cmdoption:: -r , --ref
Specify that you are interested in the **Reference** (cleaned to keep only high quality sequences)
version of the **Silva** database.
.. cmdoption:: -n , --nr
Specify that you are interested in the **Non redundant** version of the **Silva** database.
just a version of the to closely related sequence is kept in this version of the database
.. warning::
Non redundant version of **Silva** exists only for the SSU sequences
in its **Reference** and **Truncated** version
.. cmdoption:: -t , --trunc
Specify that you are interested in the **Truncated** (limited to the rDNA element without flanked regions)
version of the **Silva** database.
.. cmdoption:: --local=<DIRNAME>
Specify you have already downloaded a copy of the **Silva** database located at the following URL
`<http://www.arb-**Silva**.de/no_cache/download/archive/current/Exports/>`_
*Example:*
.. code-block:: bash
> obisilva --ssu --parc --local=**Silva**Dir
This format the **SSUParc** version of the **Silva** database pre-downloaded in the `**Silva**Dir` directory.
.. include:: ../optionsSet/defaultoptions.txt
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