ruby-igv

Ruby-IGV is a simple tool for controlling the Integrated Genomics Viewer (IGV) from the Ruby language. It provides an automated way to load files, specify genome locations, and take and save screenshots using IGV.

Installation

Requirement :

• Ruby
• IGV (Integrative Genomics Viewer)
  • Enable IGV to listen on the port
  • View > Preference > Advanced > Enable port ☑

gem install ruby-igv

Quickstart

require 'igv'

igv = IGV.start # This launch IGV

igv.set      :SleepInterval, 200 # give a time interval
igv.genome   'hg19'
igv.load     'http://hgdownload.cse.ucsc.edu/goldenPath/' \
             'hg19/encodeDCC/wgEncodeUwRepliSeq/' \
             'wgEncodeUwRepliSeqK562G1AlnRep1.bam'
igv.go       'chr18:78016233-78016640'
igv.snapshot 'region.png'

Usage

commands

The commonly used commands in IGV are summarized in the official list of Batch commands. (but even this does not seem to be all of them). You can also call the commands method from Ruby to open a browser and view the list.

igv.commands # Show the IGV command reference in your browser

docs

See docs. Not all commands are implemented in Ruby.

send

Commands that are not implemented can be sent using the send method.

igv.send("maxPanelHeight", 10)

Launch IGV

Launch IGV from Ruby script.

igv = IGV.start # launch IGV app using spawn

Open socket connection to IGV

igv = IGV.new   # create an IGV object. Then you will type `igv.connect`
igv = IGV.open  # create an IGV object and connect it to an already activated IGV.

Close IGV

The behavior of the following methods is different.

igv.close       # close the socket connection
igv.exit        # send exit command to IGV then close the socket connection
igv.quit        # alias method to exit
igv.kill        # kill group pid created with IGV.start

Contributing

• Report bugs
• Fix bugs and submit pull requests
• Write, clarify, or fix documentation
• Suggest or add new features

Do you need commit rights to my repository?
Do you want to get admin rights and take over the project?
If so, please feel free to contact me @kojix2.

Acknowledgement

This gem is strongly inspired by a Python script developed by Brent Pedersen.

• brentp/bio-playground/igv.

License

The gem is available as open source under the terms of the MIT License.