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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


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