Plasmidviewer is a Python library to visualize plasmid maps from GenBank. This library provides only the function to visualize circular plasmids and doesn't provide functions to edit nucleotides and sequence features. If you want to do such operations, please use QUEEN, which I have recently developed. (In fact, this library is implemented based on the visualization function of QUEEN)
You can install this library using the following single command:
pip install git+https://github.com/ponnhide/plasmidviewer.git
import plasmidviewer as pv
from Bio import SeqIO
record = SeqIO.read("../example_data/addgene-plasmid-63592-sequence-334654.gbk", format="genbank")
feats = []
facecolors = []
edgecolors = []
labelcolors = []
for feat in record.features:
if feat.type == "source" or feat.type == "primer_bind":
pass
else:
feats.append(feat)
if feat.type == "CDS" and feat.strand >= 0:
facecolors.append("#FFDFDF")
edgecolors.append("#EE0000")
labelcolors.append("#DD0000")
elif feat.type == "CDS" and feat.strand == -1:
facecolors.append("#DFDFFF")
edgecolors.append("#0000EE")
labelcolors.append("#0000DD")
else:
edgecolors.append(None)
labelcolors.append(None)
facecolors.append(None)
fig, ax = pv.visualize(record, feature_list=feats, title="lentiCas9-EGFP")
fig.savefig("test1.pdf")
fig, ax = pv.visualize(record, feature_list=feats, edgecolor=edgecolors, title="lentiCas9-EGFP")
fig.savefig("test2.pdf")
fig, ax = pv.visualize(record, feature_list=feats, facecolor=facecolors, edgecolor=edgecolors, labelcolor=labelcolors, title="lentiCas9-EGFP", inner_diameter=500, tick_interval=1000)
fig.savefig("test3.pdf") 