.. COAST documentation master file, created by
   sphinx-quickstart on Tue Jul 13 21:25:51 2021.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

COAST
=================================

.. toctree::
   :maxdepth: 2
   :caption: Contents:

Introduction
____________

COAST is an alignment search tool that identifies similar proteomes in BLAST or diamond databases.
It does this by cumulatively identifying similar proteins for a user provided proteome and aggregating selected best hits.

The current prototype can be downloaded at:
::

      conda install -c bioconda coast=0.2.2

There are galaxy tools and auxiliar data managers in `COAST - Galaxy Tools <https://gitlab.com/coast_tool/COAST_galaxy_tools>`_

   **Cautions selecting the database**

   In the future this space will have further indications on how to best select a database fitting for your use.

Operation
_________

Currently, COAST provides the following command line programs:

- ``coast search`` \execute searches. :doc:`Know more </tools/search>`
- ``coast report`` \generates reports and aggregated metrics. :doc:`Know more </tools/report>`
- ``coast retrieve`` \retrieves reference proteomes. :doc:`Know more </tools/retrieve>`
- ``coast compare`` \reciprocal best hits between proteomes. :doc:`Know more </tools/compare>`

The following commands are meant to be examples of what a query using COAST looks like, using more advanced options.::

   # Query the proteome in MN908947.3.gb
   coast search MN908947.3.gb nr --taxidlist taxonomic_filters/10239_2021.06.11_12.34.25.txids --out . --outfmt b a

   # Generate a report without hypothetical proteins
   coast report MN908947.3.gb  MN908947.3_COAST_2021_06_25_13_10_12/blast_results.tab --out MN908947.3_COAST_2021_06_25_13_10_12/filtered/ --outfmt b a r


Credits
_______

The version 0.1, was developed during the "Project in Bioinformatics" class of the Masters in Bioinformatics at Universidade do Minho, during the spring of 2021.
The project was oriented by `Oscar Dias <https://www.ceb.uminho.pt/People/Details/73954a25-f8a7-4a3d-9baa-83939b250a74>`_ and `Sílvio Santos <https://www.ceb.uminho.pt/People/Details/45031c66-e7a2-494a-ab99-c86605462dec>`_.
The software development and testing was done by Diogo Macedo.

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Tools:

   tools/search
   tools/report
   tools/retrieve
   tools/compare

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: About Coast:

   about/academic_work
   about/contrib