Controlling IGV through a Port: my notebook.

A protocol for interacting with the The Integrative Genomics Viewer (IGV) is described here: http://www.broadinstitute.org/igv/PortCommands. So, you can save some pictures of a genomic region without interacting with IGV.

Via a shell script

$ cat script.sh

mkdir -p /tmp/igv
sleep 2
echo "snapshotDirectory /tmp/igv"
sleep 2
echo "goto chr3:100"
sleep 2
echo "snapshot"
sleep 2
echo "goto chr3:200-300"
sleep 2
echo "snapshot"
sleep 2

invoke the script

$ sh script.sh |  telnet 127.0.0.1 60151
Trying 127.0.0.1...
Connected to srv-clc-02.irt.univ-nantes.prive (127.0.0.1).
Escape character is '^]'.
INFO [2011-07-27 17:58:16,680]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:18,685]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:18,687]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_80_119.png
INFO [2011-07-27 17:58:20,787]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:22,792]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:22,794]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_200_300.png
Connection closed by foreign host.

Via java

The code

import java.io.*;
import java.net.*;
class Test
{
public static void main(String[] args) throws Exception
 {
 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("snapshotDirectory /tmp/igv");
  System.out.println(in.readLine());
        out.println("goto chr3:100");
        System.out.println(in.readLine());
 
      out.println("snapshot");
 System.out.println(in.readLine());

 in.close();
 out.close();
 socket.close();
 }
}

Compile and execute:

$ javac Test
$ java Test
INFO [2011-07-27 18:01:15,706]  [CommandExecutor.java:124] [Thread-6]  OK
OK

INFO [2011-07-27 18:01:17,711]  [CommandExecutor.java:124] [Thread-6]  OK
OK

INFO [2011-07-27 18:01:17,729]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_80_119.png
INFO [2011-07-27 18:01:20,533]  [CommandExecutor.java:124] [Thread-6]  OK
OK