.. suvtk documentation master file, created by
   sphinx-quickstart on Tue Mar 11 16:53:45 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

``suvtk`` documentation
=======================

This is the documentation for the Submission of Uncultivated Viral genomes toolkit or ``suvtk`` (/ɛs juː viː tiː keɪ/).

Installation
------------
1. To install the package, run one of the following commands depending on your preferred package manager.
   The package is available on |Bioconda| and |PyPI|, so you can use either ``conda`` or ``mamba`` for installation. 
   You can also install it using ``pip`` or from the source code for development purposes.:

.. tab-set::

   .. tab-item:: conda

      .. code-block:: none

         conda create -n suvtk -c bioconda -c conda-forge suvtk
         conda activate suvtk
         suvtk --help

   .. tab-item:: mamba

      .. code-block:: none

         mamba create -n suvtk -c bioconda -c conda-forge suvtk
         mamba activate suvtk
         suvtk --help

   .. tab-item:: pip

      .. code-block:: none

         pip install suvtk
         suvtk --help

      .. warning::

         The pip installation does not include non-python dependencies like
         |MMseqs2| and |table2asn|. You will need to install them separately.

   .. tab-item:: development

      .. code-block:: none

         git clone https://github.com/LanderDC/suvtk.git
         cd suvtk
         mamba create -n suvtk -c bioconda -c conda-forge 'python>=3.9' pip mmseqs2 table2asn
         mamba activate suvtk
         pip install -e .

2. Download the database with:

.. code-block:: none

   suvtk download-database

Or manually download and extract it from |Zenodo|.

Background
----------

The idea behind this package is to provide a toolkit to more easily submit viral sequences to Genbank. The package is designed to be user-friendly and provide a simpler experience by combining multiple resources. 
For example, ``suvtk`` follows |MIUVIG| and |ICTV_guidelines| for the submission of uncultivated viral genomes and provides the ``suvtk table2asn`` subcommand as a wrapper around NCBI's |table2asn| that only uses the necessary functionality for UViG submissions.

.. only:: html

   .. image:: _static/suvtk_diagram_light.svg
      :alt: suvtk workflow diagram
      :align: center
      :class: only-light

   .. image:: _static/suvtk_diagram_dark.svg
      :alt: suvtk workflow diagram
      :align: center
      :class: only-dark

Submission
----------

Once you have your .sqn file generated by :doc:`suvtk table2asn <help/table2asn>`, you can submit it to Genbank by mailing it to `gb-sub@ncbi.nlm.nih.gov <mailto:gb-sub@ncbi.nlm.nih.gov>`_.

Acknowledgements
----------------
A big thank you to:

* |Antônio Camargo| for the |taxonomy database|.
* |Martin Steinegger| and colleagues for |MMseqs2| and |BFVD|.

.. |Bioconda| raw:: html

   <a href="https://bioconda.github.io/recipes/suvtk/README.html" target="_blank">Bioconda</a>

.. |PyPI| raw:: html

   <a href="https://pypi.org/project/suvtk/" target="_blank">PyPI</a>

.. |Zenodo| raw:: html

   <a href="https://doi.org/10.5281/zenodo.15374439" target="_blank">Zenodo</a>

.. |MIUVIG| raw:: html

   <a href="https://www.nature.com/articles/nbt.4306" target="_blank">MIUVIG</a>

.. |ICTV_guidelines| raw:: html

   <a href="https://static-content.springer.com/esm/art%3A10.1038%2Fs41587-023-01844-2/MediaObjects/41587_2023_1844_MOESM1_ESM.pdf" target="_blank">ICTV guidelines</a>

.. |table2asn| raw:: html

   <a href="https://www.ncbi.nlm.nih.gov/genbank/table2asn/" target="_blank">table2asn</a>

.. |Antônio Camargo| raw:: html

   <a href="https://github.com/apcamargo" target="_blank">Antônio Camargo</a>

.. |taxonomy database| raw:: html

   <a href="https://github.com/apcamargo/ictv-mmseqs2-protein-database" target="_blank">taxonomy database</a>

.. |Martin Steinegger| raw:: html

   <a href="https://github.com/steineggerlab" target="_blank">Martin Steinegger</a>

.. |MMseqs2| raw:: html

   <a href="https://github.com/soedinglab/MMseqs2" target="_blank">MMseqs2</a>

.. |BFVD| raw:: html

   <a href="https://bfvd.steineggerlab.workers.dev/" target="_blank">BFVD</a>


.. toctree::
   :maxdepth: 1
   :hidden:

   suvtk <self>
   
.. toctree::
   :maxdepth: 1
   :caption: Commands
   :hidden:

   help/taxonomy
   help/features
   help/virus-info
   help/co-occurrence
   help/gbk2tbl
   help/comments
   help/table2asn

.. toctree::
   :maxdepth: 1
   :caption: Python API
   :hidden:

   source/modules