Plasmidviewer

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)

Installation

You can install this library using the following single command:
pip install git+https://github.com/ponnhide/plasmidviewer.git

Example code

= 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") ">

    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")

Python library to visualize circular plasmid maps

Related tags

Overview

Plasmidviewer

Installation

Example code

Example images

Owner

Mori Hideto

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