Visualization of a custom plasmid

This script shows how Feature objects are displayed in a plasmid map by using a custom ‘toy’ Annotation.

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

import matplotlib.pyplot as plt
import biotite.sequence as seq
import biotite.sequence.graphics as graphics

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()