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

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

.. _sphx_glr_examples_gallery_sequence_plasmid_map_custom.py:


Visualization of a custom plasmid
=================================

.. currentmodule:: biotite.sequence

This script shows how :class:`Feature` objects are displayed in a
plasmid map by using a custom 'toy' :class:`Annotation`. 

.. GENERATED FROM PYTHON SOURCE LINES 10-138



.. image-sg:: /examples/gallery/sequence/images/sphx_glr_plasmid_map_custom_001.png
   :alt: plasmid map custom
   :srcset: /examples/gallery/sequence/images/sphx_glr_plasmid_map_custom_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

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


    annotation = seq.Annotation([
        seq.Feature(
            "source",
            [seq.Location(0, 1500)],
            {"organism": "Escherichia coli"}
        ),

        # Ori
        seq.Feature(
            "rep_origin",
            [seq.Location(600, 700, seq.Location.Strand.REVERSE)],
            {"regulatory_class": "promoter", "note": "MyProm"}
        ),

        # Promoter
        seq.Feature(
            "regulatory",
            [seq.Location(1000, 1060)],
            {"regulatory_class": "promoter", "note": "MyProm"}
        ),
        seq.Feature(
            "protein_bind",
            [seq.Location(1025, 1045)],
            {"note": "repr"}
        ),

        # Gene A
        seq.Feature(
            "regulatory",
            [seq.Location(1070, 1080)],
            {"regulatory_class": "ribosome_binding_site"}
        ),
        seq.Feature(
            "CDS",
            [seq.Location(1091, 1150)],
            {"product": "geneA"}
        ),

        # Gene B
        seq.Feature(
            "regulatory",
            [seq.Location(1180, 1190)],
            {"regulatory_class": "ribosome_binding_site"}
        ),
        seq.Feature(
            "CDS",
            [seq.Location(1201, 1350)],
            {"product": "geneB"}
        ),
        seq.Feature(
            "regulatory",
            [seq.Location(1220, 1230)],
            {"regulatory_class": "ribosome_binding_site"}
        ),
        seq.Feature(
            "CDS",
            [seq.Location(1240, 1350)],
            {"product": "geneB2"}
        ),

        # Gene C
        seq.Feature(
            "regulatory",
            [seq.Location(1380, 1390)],
            {"regulatory_class": "ribosome_binding_site"}
        ),
        seq.Feature(
            "CDS",
            # CDS extends over periodic boundary -> two locations
            [seq.Location(1, 300), seq.Location(1402, 1500)],
            {"product": "geneC"}
        ),

        # Terminator
        seq.Feature(
            "regulatory",
            [seq.Location(310, 350)],
            {"regulatory_class": "terminator", "note": "MyTerm"}
        ),

        # Primers
        # The labels will be too long to be displayed on the map
        # If you want to display them nevertheless, set the
        # 'omit_oversized_labels' to False
        seq.Feature(
            "primer_bind",
            [seq.Location(1385, 1405)],
            {"note": "geneC"}
        ),
        seq.Feature(
            "primer_bind",
            [seq.Location(345, 365, seq.Location.Strand.REVERSE)],
            {"note": "geneC_R"}
        ),

        # Terminator
        seq.Feature(
            "regulatory",
            [seq.Location(310, 350)],
            {"regulatory_class": "terminator", "note": "MyTerm"}
        ),
    ])


    fig = plt.figure(figsize=(8.0, 8.0))
    ax = fig.add_subplot(111, projection="polar")
    graphics.plot_plasmid_map(
        ax, annotation, plasmid_size=1500, label="My plasmid",
        label_properties={"fontsize": 8}
    )

    ticks = ax.get_xticks()
    labels = ax.get_xticklabels()

    fig.tight_layout()
    plt.show()


.. _sphx_glr_download_examples_gallery_sequence_plasmid_map_custom.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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