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

.. only:: html

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

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

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

.. _sphx_glr_examples_gallery_sequence_read_quality.py:


Quality of sequence reads
=========================

This script plots the sequencing quality scores from an FASTQ file along
with the sequence (base calls).

.. GENERATED FROM PYTHON SOURCE LINES 8-49



.. image-sg:: /examples/gallery/sequence/images/sphx_glr_read_quality_001.png
   :alt: read quality
   :srcset: /examples/gallery/sequence/images/sphx_glr_read_quality_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    # Code source: Patrick Kunzmann
    # License: BSD 3 clause

    from io import StringIO
    import numpy as np
    import matplotlib.pyplot as plt
    import biotite
    import biotite.sequence as seq
    import biotite.sequence.io.fastq as fastq


    # Sample FASTQ file from https://en.wikipedia.org/wiki/FASTQ_format
    fastq_content = StringIO("""
    @SEQ_ID
    GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
    +
    !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
    """)


    fastq_file = fastq.FastqFile.read(fastq_content, offset="Sanger")
    sequence, scores = fastq.get_sequence(fastq_file, "SEQ_ID")
    figure, ax = plt.subplots(figsize=(8.0, 2.0))
    ax.bar(
        x=np.arange(len(sequence)), height=scores, color=biotite.colors["orange"],
        width=1.0, linewidth=1, edgecolor="white"
    )
    # -1 to put space between Y-axis and sequence
    ax.set_xlim(-1, len(sequence))
    # The range of Phred scores
    ax.set_ylim(0, 40)
    ax.set_ylabel("Phred score")
    ax.spines["right"].set_visible(False)
    ax.spines["top"].set_visible(False)
    ax.spines["bottom"].set_visible(False)
    # Show sequence as X-axis ticks
    ax.set_xticks(np.arange(len(sequence)))
    ax.set_xticklabels(sequence.symbols)
    ax.xaxis.set_ticks_position("none") 
    figure.tight_layout()
    plt.show()

.. _sphx_glr_download_examples_gallery_sequence_read_quality.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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