How to operate IGV using socket communication, and the story of making a Ruby Gem using that method

Introduction

IGV is software called a genome browser. You can browse various files such as the bam file of the aligned read, the bed file in which the position information on the genome is annotated, and the gff3 file in which the genetic information is written. If you have been involved in bioinformatics, you probably know this software.

IGV repository on Github

• The image is from IGV homepage

Although it is such an IGV, it may take some time to operate it while clicking with the mouse.

• Specify the reference genome
• Load the required file
• Look around the places you are paying attention to one by one
• Take a screenshot and save it as an image

It's fun to check the results visually, and I think it's a very important task, but on the other hand, I also want to automate routine tasks as much as possible. Therefore, consider operating the IGV from a programming language.

• Recently, it seems that igv.js made with JavaScript has been actively developed and widely used. .. This is not covered in this article due to insufficient research. (But eventually I'd like to make a Qiita article.)

Operate IGV using socket communication

In fact, IGV can be operated from port 60151 using socket communication.

There is a tab called advanced in View> Preference on the menu bar. If Enable port is not checked, check here.

You will then be able to use port 60151 to steer the IGV using socket communication.

List of commands that can be used to operate IGV

I translated the official reference into Japanese using DeepL Translator.

• Controlling IGV through a Port

Manipulate IGV from a programming language

Java

Since IGV is software developed in Java, the official example is also written in Java.

  Socket socket = new Socket("127.0.0.1", 60151);
  PrintWriter out = new PrintWriter(socket.getOutputStream(), true);
  BufferedReader in = new BufferedReader(new InputStreamReader(socket.getInputStream()));

  out.println("load na12788.bam,n12788.tdf");
  String response = in.readLine();
  System.out.println(response);

  out.println("genome hg18");
  response = in.readLine();
  System.out.println(response);

  out.println("goto chr1:65,827,301");
  //out.println("goto chr1:65,839,697");
  response = in.readLine();
  System.out.println(response);

  out.println("snapshotDirectory /screenshots");
  response = in.readLine();
  System.out.println(response);

  out.println("snapshot");
  response = in.readLine();
  System.out.println(response);

R

Now, what about programming languages other than Java? If you are using R, I'm not very familiar with it, but you can use it because a library for operating IGV will be provided from around bioconductor. A little search will hit the software igvR. This seems to utilize igv.js, so it may not automatically operate the IGV on the desktop ...

Python

It's a bit old script, but igv.py created by Brent Pedersen, who has recently been energetically developing bioinformatics tools using the Nim language. -There is a tool called playground / blob / master / igv / igv.py). This is a small library that wraps the socket communication above.

Ruby

I like Ruby. ** Nani Nani? Are there few tools? Then you can make it yourself !** So, referring to Brent Pedersen's script above, I created a tool called ruby-igv that can operate IGV from Ruby language. Now you can easily operate IGV from the Ruby language.

https://github.com/kojix2/ruby-igv

The usage is like this.

igv = IGV.new

igv.load 'na12788.bam'
igv.genome 'hg18'
igv.go 'goto chr1:65,827,301'
igv.save 'image.png'

It's still a freshly made tool. If you encounter a rough cut, a bug, or find a request, please report it to issue on Github. Of course, pull requests are also welcome.

in conclusion

Not limited to bioinformatics, attention tends to be focused on how to combine existing tools to achieve the purpose and how to master the tools. And when you are making a tool, you may think that the purpose and means are reversed. But in a sense, I think it's a very selfish and narrow-minded way of thinking. The more people who make and publish tools, the more convenient, expanding and prosperous the world will be. Let's make and publish tools more freely. (Because it doesn't have to be Ruby)