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

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

.. _sphx_glr_auto_examples_plot_pipeline_stats.py:


Pipeline statistics
=====================================

.. GENERATED FROM PYTHON SOURCE LINES 8-9

First, let us get the data

.. GENERATED FROM PYTHON SOURCE LINES 9-13

.. code-block:: Python

    from sequana_pipetools.snaketools import get_pipeline_statistics

    stats = get_pipeline_statistics()





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

 .. code-block:: none

    {'coverage': 3, 'demultiplex': 11, 'denovo': 26, 'fastqc': 8, 'mapper': 19, 'quality_control': 9, 'rnaseq': 33, 'variant_calling': 33}




.. GENERATED FROM PYTHON SOURCE LINES 14-17

Plot number of rules per pipeline

Note that pacbio_qc is self-content

.. GENERATED FROM PYTHON SOURCE LINES 17-25

.. code-block:: Python

    from pylab import tight_layout, title

    stats[0].sum().plot(kind="barh")
    title("Number of rules per pipeline")
    tight_layout()

    from collections import Counter




.. image-sg:: /auto_examples/images/sphx_glr_plot_pipeline_stats_001.png
   :alt: Number of rules per pipeline
   :srcset: /auto_examples/images/sphx_glr_plot_pipeline_stats_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 26-35

Proportions of rules re-used

Amongst the rules, about a third of the rules are not used at all in the pipelines.
There are two reasons: either they were part of previous pipeline versions and
were discarded in favour of new tools, or there were used for testing and kept
in case of.

Then, we can see that a third of the rules are used only once. And finally, about
a third used more than once.

.. GENERATED FROM PYTHON SOURCE LINES 35-42

.. code-block:: Python

    from pylab import clf, pie

    count = Counter(stats[0].sum(axis=1))
    values = list(count.values())
    times = list(count.keys())
    clf()
    pie(list(count.values()), labels=["{} used {} times".format(x, y) for x, y in zip(values, times)])



.. image-sg:: /auto_examples/images/sphx_glr_plot_pipeline_stats_002.png
   :alt: plot pipeline stats
   :srcset: /auto_examples/images/sphx_glr_plot_pipeline_stats_002.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    ([<matplotlib.patches.Wedge object at 0x7b8fd114ce90>, <matplotlib.patches.Wedge object at 0x7b8fd1128f90>], [Text(-0.6858389529157668, 0.8600144944496021, '5 used 1 times'), Text(0.6858390281006222, -0.8600144344916508, '2 used 2 times')])




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

   **Total running time of the script:** (0 minutes 0.179 seconds)


.. _sphx_glr_download_auto_examples_plot_pipeline_stats.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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