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.. automodule:: obitaxonomy
:py:mod:`obitaxonomy` specific options
---------------------------------------
.. cmdoption:: -a <TAXON_INFOS>, --add-taxon=<TAXON_INFOS>
Adds a new taxon to the taxonomy. The new taxon
is described by three values separated by colons:
its scientific name, its taxonomic rank, and the
taxid of its first ancestor.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database \
-a 'Gentiana alpina':'species':49934
Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
the taxon whose taxid is 49934.
.. cmdoption:: -m <####>, --min-taxid=<####>
Minimum *taxid* for the newly added *taxid(s)*.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -m 1000000000 \
-a 'Gentiana alpina':'species':49934
Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
the taxon whose *taxid* is 49934, with a *taxid* greater than or equal to 1000000000.
.. cmdoption:: -D <TAXID>, --delete-local-taxon=<TAXID>
Deletes the local taxon with the *taxid* <TAXID> from the
taxonomic database.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -D 10000832
Deletes the local taxon with the taxid 10000832 from the taxonomic database.
.. cmdoption:: -s <SPECIES_NAME>, --add-species=<SPECIES_NAME>
Adds a new species to the taxonomy. The new species
is described by its scientific name. The genus of the
species must already exist in the database.
The species will be added under its genus.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -s 'Gentiana alpina'
Adds the species with the scientific name *Gentiana alpina* under the genus *Gentiana*.
.. cmdoption:: -f <TAXON_NAME>:<TAXID>, --add-favorite-name=<TAXON_NAME>:<TAXID>
Adds a new favorite scientific name to the taxonomy.
The new name is described by two values separated by
a colon: the new favorite name and the *taxid* of the taxon.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database \
-f 'Gentiana algida':50748
Adds the favorite scientific name *Gentiana algida* for the *taxid* 50748 in the taxonomic database.
.. cmdoption:: -F <FILE_NAME>, --file-name=<FILE_NAME>
Adds all the taxa from a sequence file in ``OBITools`` extended
doc:`fasta <../fasta>` format, and eventually their ancestors to the database
(see documentation). Each sequence record must contain the
attribute specified by the ``-k`` option.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database \
-k my_taxon_name_key -F my_sequences.fasta
Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
database, based on the scientific name contained in the ``my_taxon_name_key`` attribute.
.. cmdoption:: -k <KEY_NAME>, --key-name=<KEY_NAME>
Works with the ``-F`` option. Defines the key of the
attribute that contains the scientific name of
the taxon to be added. See example above.
.. cmdoption:: -A <ANCESTOR>, --restricting_ancestor=<ANCESTOR>
Works with the ``-F`` option. Can be a *taxid* (integer) or
a key (string). If it is a *taxid*, this *taxid* is the
default *taxid* under which the new taxon is added if
none of his ancestors are specified or can be found.
If it is a key, :py:mod:`obitaxonomy` looks for the
ancestor *taxid* in the corresponding attribute, and the
new taxon is *systematically* added under this ancestor.
By default, the restricting ancestor is the root of the
taxonomic tree for all the new taxa.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -a 33090 \
-k my_taxon_name_key -F my_sequences.fasta
Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
database, based on the scientific name contained in the ``my_taxon_name_key`` attribute. If
the genus of the new taxon cannot be found, the new taxon is added under the taxon whose
*taxid* is 33090.
.. cmdoption:: -p <PATH>, --path=<PATH>
Works with the ``-F`` option. Key of the attribute containing
the taxonomic paths of the taxa if they are in the headers of
the sequence records. The value contained in this attribute
must be of the form 'Fungi, Agaricomycetes, Thelephorales,
Thelephoraceae' with the highest ancestors first and commas
between ancestors.
*Example:*
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -p my_taxonomic_path_key \
-k my_taxon_name_key -F my_sequences.fasta
Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
database, based on the scientific name contained in the ``my_taxon_name_key`` attribute.
Each ancestor contained in the ``my_taxonomic_path_key`` attribute is added if it does not
already exist, and the new taxon is added under the latest ancestor of the path.
.. include:: ../optionsSet/taxonomyDB.txt
.. include:: ../optionsSet/defaultoptions.txt
|
