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 package built to support working with spatial data using open source python

Satellite imagery for dummies.

Fiona reads and writes geographic data files

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

Calculate & view the trajectory and live position of any earth-orbiting satellite

Obtain a GNSS position fix from an 11-millisecond raw GNSS signal snapshot

Using Global fishing watch's data to build a machine learning model that can identify illegal fishing and poaching activities through satellite and geo-location data.

Python bindings and utilities for GeoJSON

Calculate the area inside of any GeoJSON geometry. This is a port of Mapbox's geojson-area for Python

A bot that tweets info and location map for new bicycle parking added to OpenStreetMap within a GeoJSON boundary.

Bacon - Band-limited Coordinate Networks for Multiscale Scene Representation

:earth_asia: Python Geocoder

Automated download of LANDSAT data from USGS website

leafmap - A Python package for geospatial analysis and interactive mapping in a Jupyter environment.

WhiteboxTools Python Frontend

Python script to locate mobile number

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

geobeam - adds GIS capabilities to your Apache Beam and Dataflow pipelines.

Python interface to PROJ (cartographic projections and coordinate transformations library)

Python module to access the OpenCage geocoding API