=====
Usage
=====


Single community
________________


To run SMETANA on a singe community just give it a list of single-species models in SBML format:

.. code-block:: console

    $ smetana species1.xml species2.xml ...

    $ smetana *.xml


Multiple communities
____________________

You can run SMETANA on multiple communities in a single line of code. For that you need to create a table describing the
composition of each community. This table is expected to be in long format, tab-separated, with two columns:
**community id**, **organism id**. The latter should match the SBML filename (without extension). Example:

+----------+---------+
|community1|organism1|
+----------+---------+
|community1|organism2|
+----------+---------+
|community2|organism1|
+----------+---------+
|community2|organism3|
+----------+---------+

After creating this file, invoke SMETANA as follows:

.. code-block:: console

    $ smetana *.xml -c communities.tsv

Medium composition
__________________

By default, SMETANA will simulate every community using a complete medium composition. To test your communities on
different media, give it the list of media and a file containing the media compositions. You can specify multiple media
in a single command and SMETANA will run consecutively for each medium.

.. code-block:: console

    $ smetana *.xml -m M9,LB --mediadb library.tsv

For an example on how to create your own library file please check this example_.

.. _example: https://github.com/cdanielmachado/carveme/blob/master/carveme/data/input/media_db.tsv


Global vs Detailed mode
_______________________

SMETANA has two main running modes:

- Global (``-g``, ``--global``): runs MIP/MRO and is much faster, recommended when analysing multiple communities.
- Detailed (``-d``, ``--detailed``): calculates all inter-species interactions (much slower), check **Algorithms** for details.


Advanced
________

SMETANA offers other options, such as:

- Selecting different SBML *flavors* (``--flavor``)
- Changing the name/directory of your output files (``-o``, ``--output``)
- Selecting only a subset of scores to run (``-s``, ``--scores``)
- Changing your default solver (``--solver``)
- Specifying the identifier of the extracellular compartment in the models (``--ext``).
- Calculate minimal media using molecular weights (``--molweight``).
- Exclude certain compounds (e.g.: inorganic compounds) from the analysis (``--exclude``).
- Do not compute species coupling scores (allow non-growth coupled interactions) (``--no-coupling``).


For more detailed instructions please type:

.. code-block:: console

    $ smetana -h