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

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

.. _sphx_glr_auto_examples_plot_coverage.py:


Coverage module example
=============================

.. GENERATED FROM PYTHON SOURCE LINES 9-12

.. code-block:: Python

    from sequana import SequanaCoverage, sequana_data

    bedfile = sequana_data("JB409847.bed")







.. GENERATED FROM PYTHON SOURCE LINES 13-14

Reading input BED file

.. GENERATED FROM PYTHON SOURCE LINES 14-17

.. code-block:: Python

    gc = SequanaCoverage(bedfile)






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

 .. code-block:: none


    0it [00:00, ?it/s]
    1it [00:00, 214.07it/s]




.. GENERATED FROM PYTHON SOURCE LINES 18-19

Select a chromosome (first and only one in that example)

.. GENERATED FROM PYTHON SOURCE LINES 19-22

.. code-block:: Python

    chrom = gc[0]
    print(chrom)





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

 .. code-block:: none


    Chromosome length:      19795
    Sequencing depth (DOC):                    931.31 
    Sequencing depth (median):                 988.00 
    Breadth of coverage (BOC) (percent):        96.60 
    Coverage standard deviation:        237.15
    Coverage coefficient variation:       0.25




.. GENERATED FROM PYTHON SOURCE LINES 23-25

Compute running median and zscore telling the algorithm
that the chromosome is circular.

.. GENERATED FROM PYTHON SOURCE LINES 25-29

.. code-block:: Python

    chrom.running_median(n=5001, circular=True)
    chrom.compute_zscore()
    print(chrom.get_centralness())





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

 .. code-block:: none

    0.8684516291992928




.. GENERATED FROM PYTHON SOURCE LINES 30-31

Plotting

.. GENERATED FROM PYTHON SOURCE LINES 31-32

.. code-block:: Python

    chrom.plot_coverage()



.. image-sg:: /auto_examples/images/sphx_glr_plot_coverage_001.png
   :alt: plot coverage
   :srcset: /auto_examples/images/sphx_glr_plot_coverage_001.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 0.304 seconds)


.. _sphx_glr_download_auto_examples_plot_coverage.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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