igv_remote

Interacting with IGV desktop over a port with IGV batch commands in Python.

Pre-requisite

• Installation

git clone https://github.com/getzlab/igv_remote.git
cd igv_remote
pip install .

Please make sure your IGV is running with proper authorization (to access controlled-access files)

Usage

The most fundamental method is send, which accepts a string as described in igv-commands.

import igv_remote
ir = igv_remote.IGV_remote()

ir.connect()
ir.send("genome hg19")  # any port commands
ir.close()

However we also provided some wrappers for better UI, such as load, goto etc. Here is a fuller example:

import igv_remote
ir = igv_remote.IGV_remote()

# init socket
ir.connect()

# set view params
ir.set_saveopts(img_dir = "igv_snapshots/", img_basename = "test.png" ) # must be set!
ir.set_viewopts(view_type="collapsed", sort = "base" ) # optional, this view options will be passed to all view panels

# load views / snapshot
ir.load(<tumor_bam>, <normal_bam>, ...)

# view single locus
ir.goto(<chr>, <pos>)

# view multiple loci
ir.goto_multiple(chr1=<chr1>, pos1=<pos1>, chr2=<chr2>, pos2=<pos2>)

# take a snapshot
ir.snapshot()

# close socket
ir.close()

Similar structure can be found atexamples/run.py, please log in with Google account and change the BAM paths to your authorized ones. For more complex port commands that are not implemented, please use ir.send(<your port command>) or make a PR!

FAQ

• How to interact with DRS url?
  • As far as we know, IGV does not stream DRS url. However if a DRS url contains UUID, you can use UUID to generate a signed url (http://...) which IGV can acept. Detailed instructions are in igv-gdc-buddy. examples/batch_igv.py is an example utilizing such interaction.

Links

• igv port commands
• igv batch script