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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_plot_qc_example.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_plot_qc_example.py:


QC Report
===========================

Outputs quality control report from given bam files.

.. GENERATED FROM PYTHON SOURCE LINES 9-14

Creating QC Report
------------------------
Usually as a first step after receiving bam files, we want to do a quality check
and assess our data. This code generates a PDF report of important QC statistics
for long read methylation modification bam files

.. GENERATED FROM PYTHON SOURCE LINES 14-25

.. code-block:: default


    import dimelo as dm

    # first we specify the locations of our bam files
    in_bam = "../../dimelo/test/data/winnowmap_guppy_merge_subset.bam"
    sample_name = "test"
    out_dir = "../../dimelo/dimelo_test"

    # next we run the "qc_report" function
    dm.qc_report(in_bam, sample_name, out_dir)
    # now our output directory that we specified, will have a file called "test_qc_report.pdf"




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

 Out:

 .. code-block:: none


    Processing reads:   0%|          | 0/10 [00:00<?, ? batches/s]
    Processing reads:  10%|#         | 1/10 [00:00<00:05,  1.78 batches/s]
    Processing reads:  20%|##        | 2/10 [00:01<00:04,  1.92 batches/s]
    Processing reads:  30%|###       | 3/10 [00:01<00:03,  1.92 batches/s]
    Processing reads:  40%|####      | 4/10 [00:02<00:02,  2.05 batches/s]
    Processing reads:  50%|#####     | 5/10 [00:02<00:02,  2.18 batches/s]
    Processing reads:  60%|######    | 6/10 [00:02<00:01,  2.21 batches/s]
    Processing reads:  70%|#######   | 7/10 [00:03<00:01,  2.19 batches/s]
    Processing reads:  80%|########  | 8/10 [00:03<00:00,  2.05 batches/s]
    Processing reads:  90%|######### | 9/10 [00:05<00:00,  1.39 batches/s]
    Processing reads: 100%|##########| 10/10 [00:06<00:00,  1.05s/ batches]
    Processing reads: 100%|##########| 10/10 [00:06<00:00,  1.45 batches/s]
    mean length:  12202
    num reads:  3243
    num bases:  39571086
    QC report located at: ../../dimelo/dimelo_test/test_qc_report.pdf
    Database located at: ../../dimelo/dimelo_test/winnowmap_guppy_merge_subset.db





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

   **Total running time of the script:** ( 0 minutes  12.341 seconds)


.. _sphx_glr_download_auto_examples_plot_qc_example.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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