161 lines
6.5 KiB
ReStructuredText
161 lines
6.5 KiB
ReStructuredText
.. automodule:: obitaxonomy
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:py:mod:`obitaxonomy` specific options
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.. cmdoption:: -a <TAXON_INFOS>, --add-taxon=<TAXON_INFOS>
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Adds a new taxon to the taxonomy. The new taxon
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is described by three values separated by colons:
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its scientific name, its taxonomic rank, and the
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taxid of its first ancestor.
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database \
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-a 'Gentiana alpina':'species':21496
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Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
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the taxon whose taxid is 21496.
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.. cmdoption:: -m <####>, --min-taxid=<####>
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Minimum taxid for the newly added taxid(s).
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database -m 1000000000 \
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-a 'Gentiana alpina':'species':21496
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Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
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the taxon whose taxid is 21496, with a taxid greater than or equal to 1000000000.
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.. cmdoption:: -D <TAXID>, --delete-local-taxon=<TAXID>
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Deletes the local taxon with the taxid <TAXID> from the
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taxonomic database.
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database -D 10000832
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Deletes the local taxon with the taxid 10000832 from the taxonomic database.
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.. cmdoption:: -s <SPECIES_NAME>, --add-species=<SPECIES_NAME>
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Adds a new species to the taxonomy. The new species
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is described by its scientific name. The genus of the
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species must already exist in the database.
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The species will be added under its genus.
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database -s 'Gentiana alpina'
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Adds the species with the scientific name *Gentiana alpina* under the genus *Gentiana*.
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.. cmdoption:: -f <TAXON_NAME>:<TAXID>, --add-favorite-name=<TAXON_NAME>:<TAXID>
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Adds a new favorite scientific name to the taxonomy.
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The new name is described by two values separated by
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a colon: the new favorite name and the taxid of the taxon.
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database \
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-f 'Gentiana algida':10000832
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Adds the favorite scientific name *Gentiana algida* for the taxid 10000832 in the taxonomic database.
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.. cmdoption:: -F <FILE_NAME>, --file-name=<FILE_NAME>
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Adds all the taxa from a sequence file in OBITools extended
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fasta format, and eventually their ancestors to the database
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(see documentation). Each sequence record must contain the
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attribute specified by the ``-k`` option.
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database \
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-k my_taxon_name_key -F my_sequences.fasta
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Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
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database, based on the scientific name contained in the ``my_taxon_name_key`` attribute.
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.. cmdoption:: -k <KEY_NAME>, --key-name=<KEY_NAME>
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Works with the ``-F`` option. Defines the key of the
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attribute that contains the scientific name of
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the taxon to be added. See example above.
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.. cmdoption:: -A <ANCESTOR>, --restricting_ancestor=<ANCESTOR>
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Works with the ``-F`` option. Can be a taxid (integer) or
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a key (string). If it is a taxid, this taxid is the
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default taxid under which the new taxon is added if
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none of his ancestors are specified or can be found.
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If it is a key, :py:mod:`obitaxonomy`: looks for the
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ancestor taxid in the corresponding attribute, and the
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new taxon is *systematically* added under this ancestor.
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By default, the restricting ancestor is the root of the
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taxonomic tree for all the new taxa.
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database -a 33090 \
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-k my_taxon_name_key -F my_sequences.fasta
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Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
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database, based on the scientific name contained in the ``my_taxon_name_key`` attribute. If
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the genus of the new taxon can not be found, the new taxon is added under the taxon whose
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taxid is 33090.
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.. cmdoption:: -p <PATH>, --path=<PATH>
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Works with the ``-F`` option. Key of the attribute containing
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the taxonomic paths of the taxa if they are in the headers of
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the sequence records. The value contained in this attribute
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must be of the form 'Fungi, Agaricomycetes, Thelephorales,
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Thelephoraceae' with the highest ancestors first and commas
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between ancestors.
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*Example:*
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.. code-block:: bash
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> obitaxonomy -d my_ecopcr_database -p my_taxonomic_path_key \
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-k my_taxon_name_key -F my_sequences.fasta
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Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
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database, based on the scientific name contained in the ``my_taxon_name_key`` attribute.
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Each ancestor contained in the ``my_taxonomic_path_key`` attribute is added if it doesn't
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already exist, and the new taxon is added under the latest ancestor of the path.
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.. include:: ../optionsSet/taxonomyDB.txt
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.. include:: ../optionsSet/defaultoptions.txt
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