ruby-igv

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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 :

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.
Most IGV batch commands are available as Ruby methods of the same name.
If you need to use a command not directly wrapped, you can use the send method as shown below.

send

You can send any IGV batch command using the send method.

igv.send("maxPanelHeight", 10)
igv.send("scrollToTop")
igv.send("setAccessToken", "token", "host")

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

Supported IGV batch commands

Most official IGV batch commands are available as Ruby methods, including:

  • collapse, color_by, echo, exit, expand, genome, goto, group, load, max_panel_height, new, overlay, preference, region, save_session, scroll_to_top, separate, set_alt_color, set_color, set_data_range, set_log_scale, set_sequence_strand, set_sequence_show_translation, set_sleep_interval, set_track_height, snapshot_dir, snapshot, sort, squish, viewaspairs, set_access_token, clear_access_tokens

See the official IGV batch command list for details.

Return values and error handling

Most methods return the IGV response string (e.g. "OK" or an error message).
You can check the return value to handle errors or confirm success.

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

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.

License

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