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

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

.. _sphx_glr_examples_gallery_sequence_region_visualization.py:


Visualization of region in proximity to *lac* operon
====================================================

This script creates a feature map for the region around the *lac* operon
in the E. coli BL21 genome.

.. GENERATED FROM PYTHON SOURCE LINES 8-52



.. image-sg:: /examples/gallery/sequence/images/sphx_glr_region_visualization_001.png
   :alt: region visualization
   :srcset: /examples/gallery/sequence/images/sphx_glr_region_visualization_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

    import biotite.sequence as seq
    import biotite.sequence.graphics as graphics
    import biotite.sequence.io.genbank as gb
    import biotite.database.entrez as entrez
    import numpy as np
    import matplotlib.pyplot as plt

    # Download E. coli BL21 genome
    file = entrez.fetch("CP001509", None, suffix="gb",
                             db_name="nuccore", ret_type="gb")
    gb_file = gb.GenBankFile.read(file)
    _, seq_length, _, _, _, _ = gb.get_locus(gb_file)
    annotation = gb.get_annotation(gb_file, include_only=["gene"])
    # Find the minimum and maximum locations of lac genes
    min_loc = seq_length
    max_loc = 1
    for feature in annotation:
        for loc in feature.locs:
            # Ignore if feature is only a pseudo-gene (e.g. gene fragment)
            # and check if feature is lacA gene (begin of lac operon)
            if "gene" in feature.qual \
                and  "pseudo" not in feature.qual \
                and feature.qual["gene"] == "lacA":
                    if min_loc > loc.first:
                        min_loc = loc.first
                    if max_loc < loc.last:
                        max_loc = loc.last
    # Extend the location range by 1000 (arbitrary) in each direction
    min_loc -= 10000
    max_loc += 10000
    # Visualize the region as feature map

    fig = plt.figure(figsize=(8.0, 8.0))
    ax = fig.add_subplot(111)
    graphics.plot_feature_map(
        ax, annotation, loc_range=(min_loc, max_loc), symbols_per_line=2000,
        show_numbers=True, show_line_position=True
    )
    fig.tight_layout()

    plt.show()

.. _sphx_glr_download_examples_gallery_sequence_region_visualization.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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