Introduction

An IGB script file (available starting with IGB 6.3) is a simple batch file that allows a user to run sequential commands outside of IGB, either at startup (via a command-line option) or while IGB is running (via a URL "Bookmark" option -- see control bookmark). It can also be loaded via the File->Load menu (or via drag-and-drop) if its filename extension is ".igb".

The script file has a simple, space-delimited syntax.

Supported commands

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.

goto <region>

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

load <file or URL>

• Load the specified file (identified by full path) or URL into IGB.

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

• Change the load mode for the specified feature (identified by full path).

refresh

• Equivalent to clicking the Load Data button in IGB. This triggers loading of data from the files or URLs 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. Format is determined by the filename extension. Supported formats are those supported by IGB Export function. (See File > Export Image...) The filename defaults to "<genome_version><timestamp>.png" if not specified.

select <geneids>

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

sleep <milliseconds>

• Sleep the application for x milliseconds.

# Comment

• Comments.  Lines starting with '#' are ignored.

Example script