Scripting

An IGB script file (available in 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.

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 Refresh Data button in IGB. This allows the user to load data into the view.

"snapshot [<filename>]" or "snapshotwholeFrame [<filename>]"

"snapshotmainView [<filename>]"

"snapshotmainViewWithLabels [<filename>]"

"snapshotslicedViewWithLabels [<filename>]"

• Export the entire frame, main view, main view with labels, or sliced view, respectively, to a file. Format is determined by the filename extension. Supported formats are those supported by IGB Export (including but not limited to: .eps, .gif, .pdf, .png, .ps). The filename defaults to "<genome_version><timestamp>.png" if not specified.

"select <geneids>"

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

"sleep <milliseconds>"

• Sleep the application for x milliseconds.

"#"

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

Example script