Quickstart
==========

.. warning::
   We assume that you arrive at this step having installed the tool first (see :doc:`installation`), for instance in a Python virtual environment, or conda (mamba) environment.

The following quickstart guide will help you get started with MetaNetMap. Code examples are provided for each step, applying to toy data included in the repository.

Two modes are available for testing, with an option to enable or disable **partial match**.

The **Partial match** is optional, as it can be time-consuming. It is a post-processing step applied to metabolites or IDs that were not successfully mapped during the initial run. These unmatched entries are re-evaluated using specific strategies, which increase the chances of finding a match (e.g., via ChEBI, InChIKey, or enantiomer simplification).

Tests use a dedicated third-party conversion table relying on MetaCyc data. Because licence restrictions apply, we provide the possibility to create such a table using freely available MetaNetX data. This conversion datatable can be created easily using the folowing command: 

.. code-block:: bash

    metanetmap build_db --db metanetx 

Classic mode
------------

The classic mode allows you to input a single metabolomic annotation profile (tabulated file, `.maf` or `.tsv`) or a directory containing multiple metabolomic annotation profiles, and a unique metabolic network (`.sbml` or `.xml`) to which metabolites will be mapped.

.. code-block:: bash

    metanetmap test

Classic mode with partial match activated:

.. code-block:: bash

    metanetmap test --partial_match

Community mode
----------------
The **"community"** mode allows you to input a directory containing multiple metabolomic annotation profiles (tabulated files, `.maf` or `.tsv`), as well as a directory containing multiple metabolic networks (`.sbml` or `.xml`).

.. code-block:: bash

    metanetmap test --community 


Community mode with partial match activated:

.. code-block:: bash

    metanetmap test --community --partial_match

For more details on modes refer to :doc:`usage`.