:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'psytrans'
.. highlight: bash

psytrans
========

.. conda:recipe:: psytrans
   :replaces_section_title:
   :noindex:

   psytrans.py \- Parasite \& Symbiont Transcriptome Separation

   :homepage: https://github.com/rivera10/psytrans
   :license: GPLv3
   :recipe: /`psytrans <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/psytrans>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/psytrans/meta.yaml>`_

   psytrans.py separates the sequences of a host species from those of its main symbiont\(s\) or parasite\(s\) based on Support Vector Machine classification.
   The program takes as input a file in fasta format with the sequences to be classified.
   The program also requires a file with sequences of a species related to the host\, and a file with sequences related to the symbiont \(or parasite\).
   The queries will be compared to these two files using BLASTX.
   Alternatively\, the user can provide the output of pre\-computed BLASTX searches \(in tabular format\: \-outfmt 6 or 7\).
   The classification is then carried out using the command line tools from libsvm.



.. conda:package:: psytrans

   |downloads_psytrans| |docker_psytrans|

   :versions:
      
      

      ``2.0.0-1``,  ``2.0.0-0``

      

   
   :depends blast: ``>=2.2.31``
   :depends libsvm: ``>=3.16``
   :depends python: ``>3.6``
   :requirements:

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions).
  We will show all commands using mamba below, but the arguments are the same for the two
  others.

  Given that you already have a conda environment in which you want to have this package, install with::

      mamba install psytrans

   and update with::

      mamba update psytrans

  To create a new environment, run::

      mamba create --name myenvname psytrans

  with ``myenvname`` being a reasonable name for the environment
  (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

      docker pull quay.io/biocontainers/psytrans:<tag>

   (see `psytrans/tags`_ for valid values for ``<tag>``)


.. |downloads_psytrans| image:: https://img.shields.io/conda/dn/bioconda/psytrans.svg?style=flat
   :target: https://anaconda.org/bioconda/psytrans
   :alt:   (downloads)
.. |docker_psytrans| image:: https://quay.io/repository/biocontainers/psytrans/status
   :target: https://quay.io/repository/biocontainers/psytrans
.. _`psytrans/tags`: https://quay.io/repository/biocontainers/psytrans?tab=tags


.. raw:: html

    <script>
        var package = "psytrans";
        var versions = ["2.0.0","2.0.0"];
    </script>






Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/psytrans/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/psytrans/README.html