Plasmid map of a 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

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

import io
import matplotlib.pyplot as plt
import requests
import biotite
import biotite.sequence.graphics as graphics
import biotite.sequence.io.genbank as gb

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()