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

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

.. _sphx_glr_examples_gallery_sequence_plasmid_map.py:


Plasmid map of a pET15 vector
==============================

This script downloads the GenBank file for a *pET15* plasmid from
*AddGene* and draws a plasmid map using a custom feature formatter.

- **Promoters** - green arrow
- **Terminators** - red arrow
- **Protein binding sites** - light green rectangle
- **RBS** - light orange rectangle
- **CDS** - orange arrow
- **Ori** - gray arrow
- **Primer** - blue arrow

.. GENERATED FROM PYTHON SOURCE LINES 16-77



.. image-sg:: /examples/gallery/sequence/images/sphx_glr_plasmid_map_001.png
   :alt: plasmid map
   :srcset: /examples/gallery/sequence/images/sphx_glr_plasmid_map_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

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


    PLASMID_URL = "https://media.addgene.org/snapgene-media/v1.7.9-0-g88a3305/"\
                  "sequences/12250/9998fdbe-051f-4dc6-ba0f-24e65127a0c5/" \
                  "addgene-plasmid-26092-sequence-12250.gbk"


    response = requests.get(PLASMID_URL)
    gb_file = gb.GenBankFile.read(io.StringIO(response.text))
    annotation = gb.get_annotation(gb_file, include_only=[
        "promoter", "terminator", "protein_bind",
        "RBS", "CDS", "rep_origin", "primer_bind"
    ])
    _, seq_length, _, _, _, _ = gb.get_locus(gb_file)
    # AddGene stores the plasmid name in the 'KEYWORDS' field
    # [0][0][0] ->
    # The first (and only) 'KEYWORDS' field
    # The first entry in the tuple
    # The first (and only) line in the field
    plasmid_name = gb_file.get_fields("KEYWORDS")[0][0][0]


    def custom_feature_formatter(feature):
        # AddGene stores the feature label in the '\label' qualifier
        label = feature.qual.get("label")
        if feature.key == "promoter":
            return True, biotite.colors["dimgreen"], "black", label
        elif feature.key == "terminator":
            return True, "firebrick", "black", label
        elif feature.key == "protein_bind":
            return False, biotite.colors["lightgreen"], "black", label
        elif feature.key == "RBS":
            return False, biotite.colors["brightorange"], "black", label
        elif feature.key == "CDS":
            return True, biotite.colors["orange"], "black", label
        elif feature.key == "rep_origin":
            return True, "lightgray", "black", label
        elif feature.key == "primer_bind":
            return True, "blue", "black", label


    fig = plt.figure(figsize=(8.0, 8.0))
    ax = fig.add_subplot(111, projection="polar")
    graphics.plot_plasmid_map(
        ax, annotation, plasmid_size=seq_length,
        label=plasmid_name, feature_formatter=custom_feature_formatter
    )
    fig.tight_layout()
    plt.show()


.. _sphx_glr_download_examples_gallery_sequence_plasmid_map.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.ipynb <plasmid_map.ipynb>`

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

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


.. only:: html

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

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