Introduction

Starting with IGB 6.3, IGB supports a simple scripting language that contains commands related to loading data from files and URLs.

Scripts can be run

• At startup, via a command-line option. See: Command Line Arguments
• From IGB links. See: Controlling IGB using IGB Links
• Using the File > Open command (provided the file name ends with .igb)
• By drag-and-drop, dragging the file into an open IGB window

Syntax

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

Commands

Specify a genome version

genome <version>

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

Go to a region

goto <region>

Go to a region of a chromosome (e.g., "chr1:40000-60000"). Any format that's accepted by IGB is accepted here.

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.

Change the load mode for an active 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.

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.

Making images

snapshot <filename>

snapshotwholeFrame <filename>

snapshotmainView <filename>

snapshotmainViewWithLabels <filename>

snapshotslicedViewWithLabels <filename>

Export the entire frame, main view, main view with labels, or sliced view, respectively, to a an image file.

The filename extension determines the format.

Supported formats are those supported by IGB Export function. 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.

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
goto chr4:18,040,000 - 18,045,056
# load a file
load http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bam
# set load mode to region in view
loadmode REGION_IN_VIEW http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bam
# load the data
refresh