| Table of Contents |
|---|
Introduction
Starting with IGB 6.3, you You can control IGB from scripts, which are text files containing simple commands for navigation, loading data, and making snapshots.
You can To run an IGB script:
- By opening Open a script file using File > Open. Script files should end with .igb or .js for javascript.
- From Click an IGB linksscript link. See: Controlling IGB using IGB Links
- By drag-Drag and - drop , dragging the a script file into an open IGB window
...
- .
...
Syntax
The script file has a simple, space-delimited syntax. Each command should occupy a separate line.
Commands
...
Bring IGB to front
| Code Block |
|---|
bringToFront |
Bring the IGB window to the front of the user's desktop.
...
Open a genome version
| Code Block |
|---|
genome <version> |
Specify a 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.
| Code Block |
|---|
homescreen |
Return to the IGB start screen.
...
Go to a region
| Code Block |
|---|
goto <region> |
Go to a region of a chromosome (e.g., "chr1:40000-60000" or "chr1:40,000-60,000"). Commas are optional. Any region format that's accepted by the IGB is accepted herequick search text entry (top left corner) is acceptable.
...
Hide a track
| Code Block |
|---|
hidetrack <file or URL> |
Hide the track. Accepts one or more comma separated files identified by full path or URL.
Add a new data set to IGB's list of active data sets
...
Remove a data set from IGB's list of active data sets
...
| Code Block |
|---|
unload <file or URL> or deleteTrack <file or URL> |
...
This command accepts one or more comma separated files identified by full path or URL.
Unloading all data sets from IGB
| Code Block |
|---|
deleteAllTracks |
This command accepts no arguments. It removes all loaded data sets from IGB on execution, including reference annotation tracks for a genome version. To avoid removing all data sets, use unload or deleteTrack commands.
Change the load mode for an active (opened) data set
...
Change the load mode for the specified data set or file, identified by full path.
| Info |
|---|
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
...
| Code Block |
|---|
snapshotslicedViewWithLabels <filename> <absolue path to file> |
Export the entire frame, main view, main view with labels, or sliced view, respectively, to an image file.
The filename extension determines the format.
Supported formats are those supported by IGB Export function. 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.
| Info |
|---|
The snapshot and snapshotwholeFrame commands only work on Mac and Linux if attempting to export an SVG file. |
Select genes
| Code Block |
|---|
select <geneids> |
...
Lines starting with the IGB script comment character '#' are ignored.
...
Examples
Loading a BAM file
| Code Block |
|---|
# 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/quickloadrnaseq/A_thaliana_Jun_2009/cold_stress/cold_control.smSRP029896/ColdControl.bam # load the data refresh |
...