.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_kraken.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_plot_kraken.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_plot_kraken.py:


Kraken module example
=======================

In **Sequana**, we provide tools to quickly assess the taxonomic content of
a reads (FastQ). It is based on the Kraken and Krona software. **Sequana**
bridges the gap between those tools, Kraken databases and a simple interface to
get a quick taxonomic overview of the FastQ content.

For more information, please see the :mod:`sequana.kraken` module documentation.
Note that this feature is also part of the :ref:`pipeline_quality_control` pipeline.

Although we will use the **Sequana** library hereafter, note that there is also
a standalone application named **sequana_taxonomy**.

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Context
----------
running the kraken analysis takes some time so we do provide
an output directly. The output file can be analysed within
Sequana to plot a Pie chart but also Javascript Krona results
The kraken format is as follows::

   C   HISEQ:426:C5T65ACXX:5:2301:5633:7203    11234   203 0:2 11234:1 0:1 11234:1 0:2 11234:1 0:13 11234:1 0:1 11234:1 0:3 11234:1 0:16 11234:1 0:5 11234:1 0:6 11234:1 0:13 A:31 0:33 11234:1 0:29 11234:1 0:7
   C   HISEQ:426:C5T65ACXX:5:2301:5815:7120    11234   203 0:4 11234:1 0:12 11234:1 0:22 11234:1 0:1 0 11234:1 0:5 11234:1 0:7 11234:1 0:5 A:31 0:3 11234:1 0:22 11234:1 0:18 11234:1 0:24 11234:1

Each row correspond to a read in the FastQ file(s). The first column
is either C (classified) or U (unclassified) and the third column contains
the taxon the most relevant.

The taxon are not readable so we first need to get the scientific names
Besides, the lineage would be useful. This is done in Sequana using
the :class:`sequana.kraken.KrakenResults`. See following example.

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Example
--------

In the following example, we use the results of a kraken analysis. The
original toy data files contains 1500 reads mostly related to Measles virus


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.. code-block:: Python

    from sequana import KrakenResults, sequana_data

    test_file = sequana_data("test_kraken.out", "examples")
    k = KrakenResults(test_file)
    df = k.plot(kind="pie", delete_krona_file=True)
    print(df)





.. image-sg:: /auto_examples/images/sphx_glr_plot_kraken_001.png
   :alt: plot kraken
   :srcset: /auto_examples/images/sphx_glr_plot_kraken_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    name:Measles virus genotype G3                        1.010101
    name:Measles virus genotypes and isolates             3.030303
    name:Measles virus strain MVi/California.USA/8.04     8.080808
    name:Measles virus strain Edmonston-Zagreb            8.080808
    Unclassified                                         10.101010
    name:Measles virus                                   69.696970
    dtype: float64




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Note that only a subset of taxons are shown in the pie chart
that is those that cover at least 1% of the total reads. Others
are put together and labelled "others"

A more interactive plot can be obtained using Krona if installed:

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.. code-block:: Python

    from sequana import KrakenResults, sequana_data

    test_file = sequana_data("test_kraken.out", "examples")
    import easydev

    if easydev.cmd_exists("ktImportText"):
        k = KrakenResults(test_file)
        k.to_js()  # The output filame is krona.html by default








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An example is available in  `Krona example <../_static/krona.html>`_


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.070 seconds)


.. _sphx_glr_download_auto_examples_plot_kraken.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_kraken.ipynb <plot_kraken.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_kraken.py <plot_kraken.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_kraken.zip <plot_kraken.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_