IGB User's Guide
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Introduction

Starting with IGB 6.3, you can control IGB from scripts, text files containing simple commands for navigation, loading data, and making snapshots.

You can run an IGB script:

  • By opening a script file using File > Open. Script files should end with .igb.
  • From IGB links. See: Controlling IGB using IGB Links
  • By drag-and-drop, dragging the file into an open IGB window

Note: A protoype plug-in enabling python scripts (.py extension) was developed but is not yet released. If you would like to know more, please get in touch.

Syntax

The script file has a simple, space-delimited syntax. Each command should occupy a separate line.

Commands

Open a genome version

genome <version>

Open genome version (e.g., H_sapiens_Mar_2006). Any genome version or synonym that's accepted by IGB is accepted here.

Go back to the IGB start screen.

homescreen

Return to the IGB start screen.

Go to a region

goto <region>

Go to a region of a chromosome (e.g., "chr1:40000-60000" or "chr1:40,000-60,000").

Add a new data set to IGB's list of active data sets

load <file or URL>

Load the specified file (identified by full path) or URL into IGB. The data set will appear in the user's Data Management table upon completion.

Remove a data set from IGB's list of active data sets

unload <file or URL>

Change the load mode for an active (opened) data set

loadmode <NO_LOAD | REGION_IN_VIEW | CHROMOSOME | GENOME> <file or URL>

Change the load mode for the specified data set or file, identified by full path.

The loadmode command will work for any loaded track. Make sure to load your desired track before calling the loadmode command.

Load data from currently active data sets

refresh

This is equivalent to clicking the Load Data button in IGB. This triggers loading of data from the active data sets available in IGB, as specified in the load command.

Make images

snapshot <filename>

snapshotwholeFrame <filename>

snapshotmainView <filename>

snapshotmainViewWithLabels <filename>

snapshotslicedViewWithLabels <absolue path to file>

Export the entire frame, main view, main view with labels, or sliced view, respectively, to a PNG format file. You must include the full path to the file or IGB will write the file to the location from where you launched IGB.

The filename defaults to "<genome_version><timestamp>.png" if not specified.

Select genes

select <geneids>

Selects the given gene IDs, which are passed in as a comma-separated list.

Wait (sleep) for commands to finish

sleep <milliseconds>

Sleep the application for x milliseconds.

IGB is multi-threaded, which means that the user may be able to operate IGB while data are being loaded. If your IGB script includes loading data from remote sites (e.g, RNASeq data from the IGBQuickLoad.org site) then you should include a sleep command to give IGB time to load the data.

Comments

Lines starting with the IGB script comment character '#' are ignored.

Example script

# select genome
genome A_thaliana_Jun_2009
# go to a region in chr4
# commas are optional
goto chr4:8,860,484-8,872,096
# load a file
load http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bam
# load the data
refresh

 

 

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