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

Minimum Bounding Box of Geospatial data

Pure Python NetCDF file reader and writer

:earth_asia: Python Geocoder

Tools for the extraction of OpenStreetMap street network data

Bacon - Band-limited Coordinate Networks for Multiscale Scene Representation

Pure python WMS

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

Simple CLI for Google Earth Engine Uploads

Tile Map Service and OGC Tiles API for QGIS Server

A Python package for delineating nested surface depressions from digital elevation data.

A python package that extends Google Earth Engine.

Global topography (referenced to sea-level) in a 10 arcminute resolution grid

Python script that can be used to generate latitude/longitude coordinates for GOES-16 full-disk extent.

An API built to format given addresses using Python and Flask.

glTF to 3d Tiles Converter. Convert glTF model to Glb, b3dm or 3d tiles format.

Using SQLAlchemy with spatial databases

Geocoding library for Python.

Implementation of Trajectory classes and functions built on top of GeoPandas

pure-Python (Numpy optional) 3D coordinate conversions for geospace ecef enu eci

Code and coordinates for Matt's 2021 xmas tree