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 or .js for javascript.
  • 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

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.

Unloading a data set from IGB

unload <file or URL>

or
deleteTrack <file or URL>

This command accepts one or more comma separated files identified by full path or URL. If a matching track is found for the specifed URL/path it will be deleted.

 

Unloading all data sets from IGB

deleteAllTracks

This command accepts no arguments, and will remove all loaded data sets from IGB on execution (note: including default annotation tracks for a genome version).  To avoid removing all data sets, see the unload or deleteTrack commands as an alternative.

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.

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 <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.

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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