kojix2/ruby-igv

Simple wrapper to the IGV socket interface

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

IGV batch 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 yard docs. Commonly used IGV batch commands can be called from Ruby methods of the same name. However, not all IGV batch commands are implemented in Ruby. Use the send method described below.

send

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

igv.send("maxPanelHeight", 10)

To avoid unexpected behavior, ruby-igv does not use the method_missing mechanism.

Launch IGV

Launch IGV from Ruby script.

igv = IGV.start # launch IGV app using spawn

You can specify the port.

igv = IGV.start(port: 60152)

If you start IGV in this way, you can force IGV to terminate by calling the kill method.

igv.kill

Open socket connection to IGV

If IGV is already running, use new or open.

new

igv = IGV.new   # create an IGV object. Then you will type `igv.connect`
igv = IGV.new(host: "127.0.0.1", port: 60151, snapshot_dir: "~/igv_snapshot")
igv.connect # To start a connection, call connect explicitly.
igv.close

open

igv = IGV.open  # create an IGV object and connect it to an already activated IGV.
igv.close
IGV.open(host: "127.0.0.1", port: 60151, snapshot_dir: "~/igv_snapshot") do |igv|
  # do something
end # The socket is automatically closed.

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 this 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.

ruby-igv's Issues

Images

Removed

Implementation

• collapse
• colorBy
• echo
• exit
• expand
• genome
• goto
• group
• load
• maxPanelHeight
• new <- clear?
• overlay
• preference
• region
• saveSession
• separate
• setAltColor
• setColor
• setDataRange
• setLogScale
• setSequenceStrand
• setSequenceShowTranslation
• setSleepInterval
• setTrackHeight
• snapshotDirectory
• snapshot
• sort
• squish
• viewaspairs