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

A python package that extends Google Earth Engine.

Advanced raster and geometry manipulations

Map Ookla server locations as a Kernel Density Estimation (KDE) geographic map plot.

Django model field that can hold a geoposition, and corresponding widget

This GUI app was created to show the detailed information about the weather in any city selected by user

Xarray backend to Copernicus Sentinel-1 satellite data products

iNaturalist observations along hiking trails

Read images to numpy arrays

Code and coordinates for Matt's 2021 xmas tree

A compilation of several single-beam bathymetry surveys of the Caribbean

GeoNode is an open source platform that facilitates the creation, sharing, and collaborative use of geospatial data.

A library to access OpenStreetMap related services

Digital Earth Australia notebooks and tools repository

Geographic add-ons for Django REST Framework. Maintained by the OpenWISP Project.

Python module to access the OpenCage geocoding API

gjf: A tool for fixing invalid GeoJSON objects

Satellite imagery for dummies.

Centroids as a Service

PySAL: Python Spatial Analysis Library Meta-Package

Interactive Maps with Geopandas