.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_bam.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_bam.py>`
        to download the full example code.

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

.. _sphx_glr_auto_examples_plot_bam.py:


BAM module example
==================

Plot histogram of MAPQ values contained in a BAM file

.. GENERATED FROM PYTHON SOURCE LINES 10-13

Get a data set (BAM file) for testing
################################################
 first import the relevant modules

.. GENERATED FROM PYTHON SOURCE LINES 13-17

.. code-block:: Python

    from sequana import BAM, sequana_data

    datatest = sequana_data("test.bam", "doc")








.. GENERATED FROM PYTHON SOURCE LINES 18-19

Use :class:`sequana.bamtools.BAM` class to plot the MAPQ historgram

.. GENERATED FROM PYTHON SOURCE LINES 19-28

.. code-block:: Python

    b = BAM(datatest)
    b.plot_bar_mapq()


    # for some unknown reasons, we must call show in this example for this image to
    # appear in the doc
    from pylab import show

    show()



.. image-sg:: /auto_examples/images/sphx_glr_plot_bam_001.png
   :alt: plot bam
   :srcset: /auto_examples/images/sphx_glr_plot_bam_001.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 0.372 seconds)


.. _sphx_glr_download_auto_examples_plot_bam.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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