Skip to main content

python interface to IGV that simplifies creating screenshots of BAMs, VCFs, BEDs, etc for one-off spot checking or automated / scripted image collection

Project description

Overview

Python interface to IGV - inspired by an IGV_plotter tool originally written by @tmfromer.

It includes the following executables:

  • igv Launches IGV from the command line and optionally makes it load some file(s) and jump to some locus.
  • igv_plotter Automates taking IGV screenshots of one or more data files at one or more loci.
  • igvweb_viewer Allows bam, vcf, and/or bed file tracks to be viewed in a web browser using igv.js.

Install

  • To install for all users, run: pip install igv_plotter
  • To install in your home directory (eg. if you don’t have permissions to install for all users), add ~/.local/bin to your PATH and run: pip install igv_plotter --user

Run

To see all command line options, you can do:

igvweb_viewer -h

igv_plotter -h

igv -h

igvweb_viewer script - usage example:

This starts a webserver for viewing 3 files at 2 loci:

igvweb_viewer my_file1.vcf my_file2.bam my_file3.bed 1:12345 chrX:12345

After starting this script, open your web browser to 127.0.0.1:8000 for an interactive browser-based IGV view of these files.

igv_plotter script - usage example:

This loads 3 files, and takes 2 snapshots:

igv_plotter my_file1.vcf my_file2.bam my_file3.bed 1:12345 chrX:12345

igv script - usage example:

This launches IGV with 2 files loaded at locus 1:12345:

igv my_file1.vcf my_file3.bed 1:12345

Configure

An ~/.igv_plotter config file can be created and used to persitantly set any igv_plotter or igv command line options, by using lines like: <command line option (without --)> = <value>

Contribute

https://travis-ci.org/macarthur-lab/igv_utils.svg?branch=master

Issue reporting and pull requests are appreciated.

Unit tests can be run with:

python setup.py test

This code is open sourced under the MIT license.

Project details


Release history Release notifications

This version
History Node

0.9.8.7

History Node

0.9.8.6

History Node

0.9.8.4

History Node

0.9.8.3

History Node

0.9.8.2

History Node

0.9.8.1

History Node

0.9

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
igv_plotter-0.9.8.7.tar.gz (28.7 MB) Copy SHA256 hash SHA256 Source None Dec 23, 2016

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page