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:py:mod:`ecofind`: querying a taxonomic database
================================================
:py:mod:`ecofind` retrive taxonomic information from taxonomic database
given either a *taxid* or a regular expression patterns.
:py:mod:`ecofind` specific options
----------------------------------
.. cmdoption:: -d <filename>
Filename containing the database used for the *in silico* PCR. The database
must be in the ``ecoPCR format`` (see :doc:`obiconvert <./obiconvert>`).
.. WARNING:: This option is compulsory.
.. cmdoption:: -a
Enable the search on all alternative names and not only scientific names.
.. cmdoption:: -L
List all taxonomic rank available for -r option and exit.
.. cmdoption:: -r
Restrict to given taxonomic rank.
.. cmdoption:: -s
Displays all subtree's information for the given taxid.
.. cmdoption:: -p
Displays all parental tree's information for the given taxid.
.. cmdoption:: -P
Display taxonomic Path as suplementary column in output
.. cmdoption:: -h
Print help.
Output file
-----------
The output file contains several columns, with '|' as separator, and describes
the properties of the retrieved *taxids*.
column 1: the *taxid*
column 2: the taxonomic rank
column 3: the name (not only scientific)
column 4: class name
column 5: the scientific name
column 6 (optional): the full taxonomic path of the *taxid*
Examples
--------
*Example 1:*
.. code-block:: bash
> ecofind -d mydatabase 'homo ' > homo_.tax
Retrieve all *taxids* whose 'homo ' is contained in the associated names.
*Example 2:*
.. code-block:: bash
> ecofind -d mydatabase -p 9606 -P > sapiens.info.tax
Retrieve all parents taxa of the 9606 *taxid*. The -P option add a supplementary column
with the full path for each *taxid*.
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