This commit is contained in:
Aurelie Bonin
@ -16,30 +16,30 @@
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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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-a 'Gentiana alpina':'species':49934
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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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the taxon whose taxid is 49934.
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.. cmdoption:: -m <####>, --min-taxid=<####>
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Minimum taxid for the newly added taxid(s).
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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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-a 'Gentiana alpina':'species':49934
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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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the taxon whose *taxid* is 49934, 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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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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@ -71,22 +71,22 @@
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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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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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-f 'Gentiana algida':50748
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Adds the favorite scientific name *Gentiana algida* for the taxid 10000832 in the taxonomic database.
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Adds the favorite scientific name *Gentiana algida* for the *taxid* 50748 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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Adds all the taxa from a sequence file in ``OBITools`` extended
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doc:`fasta <../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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@ -110,12 +110,12 @@
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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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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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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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@ -129,8 +129,8 @@
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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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the genus of the new taxon cannot 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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@ -151,7 +151,7 @@
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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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Each ancestor contained in the ``my_taxonomic_path_key`` attribute is added if it does not
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already exist, and the new taxon is added under the latest ancestor of the path.
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@ -1,11 +1,11 @@
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#!/usr/local/bin/python
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'''
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:py:mod:`obitaxonomy`: Manages taxonomic databases
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:py:mod:`obitaxonomy`: manages taxonomic databases
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==================================================
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.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org> and Celine Mercier <celine.mercier@metabarcoding.org>
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The :py:mod:`obitaxonomy` command can generate an ecopcr database from a NCBI taxdump
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The :py:mod:`obitaxonomy` command can generate an ecoPCR database from a NCBI taxdump
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(see NCBI ftp site) and allows managing the taxonomic data contained in both types of
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database.
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@ -14,12 +14,12 @@ Several types of editing are possible:
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**Adding a taxon to the database**
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The new taxon is described by three values:
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its scientific name, its taxonomic rank, and the taxid of its first ancestor.
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its scientific name, its taxonomic rank, and the *taxid* of its first ancestor.
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Done by using the ``-a`` option.
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**Deleting a taxon from the database /MARCHE PAS/**
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**Deleting a taxon from the database**
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Erases a local taxon. Done by using the ``-D`` option and specifying a taxid.
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Erases a local taxon. Done by using the ``-D`` option and specifying a *taxid*.
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**Adding a species to the database**
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@ -27,15 +27,15 @@ Several types of editing are possible:
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added under its genus. Done by using the ``-s`` option and specifying a species
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scientific name.
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**Adding a preferred scientific name for a taxon in the database (????)**
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**Adding a preferred scientific name for a taxon in the database**
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Adds a preferred name for a taxon in the taxonomy, by specifying the new favorite
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name and the taxid of the taxon whose preferred name should be changed (???).
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name and the *taxid* of the taxon whose preferred name should be changed.
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Done by using the ``-f`` option.
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**Adding all the taxa from a sequence file in OBITools extended fasta format to the database**
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**Adding all the taxa from a sequence file in the `<60>BITools`` extended :doc:`fasta <../fasta>` format to the database**
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All the taxon from a file in :doc:`OBITools extended fasta format <../fasta>`, and eventually their ancestors, are added to the
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All the taxon from a file in the `<60>BITools`` extended :doc:`fasta <../fasta>` format, and eventually their ancestors, are added to the
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taxonomy database.
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The header of each sequence record must contain the attribute defined by the
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@ -45,10 +45,10 @@ Several types of editing are possible:
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A taxonomic path for each sequence record can be specified with the ``-p`` option,
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as the attribute key that contains the taxonomic path of the taxon to be added.
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A restricting ancestor can be specified with the ``-A`` option, either as a taxid
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(integer) or a key (string). If it is a taxid, this taxid is the default taxid
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A restricting ancestor can be specified with the ``-A`` option, either as a *taxid*
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(integer) or a key (string). If it is a *taxid*, this *taxid* is the default *taxid*
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under which the new taxon is added if none of his ancestors are specified or can
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be found. If it is a key, :py:mod:`obitaxonomy`: looks for the ancestor taxid in
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be found. If it is a key, :py:mod:`obitaxonomy` looks for the ancestor *taxid* in
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the corresponding attribute, and the new taxon is systematically added under this
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ancestor. By default, the restricting ancestor is the root of the taxonomic tree for
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all the new taxa.
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@ -58,15 +58,14 @@ Several types of editing are possible:
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genus in the taxonomic database. If the genus is found, the new taxon is added under it.
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If not, it is added under the restricting ancestor.
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It is highly recommended to check what was exactly done by reading the output,
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since :py:mod:`obitaxonomy` tries to be clever about what is done but can make
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mistakes.
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It is highly recommended checking what was exactly done by reading the output,
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since :py:mod:`obitaxonomy` uses *ad hoc* parsing and decision rules.
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Done by using the ``-F`` option.
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**Notes:**
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- When a taxon is added, a new taxid is assigned to it. The minimum for the new taxids
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- When a taxon is added, a new *taxid* is assigned to it. The minimum for the new *taxids*
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can be specified by the ``-m`` option and is equal to 10000000 by default.
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- For each modification, a line is printed with details on what was done.
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