An IGB script file 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 during the run (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".
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Introduction
You can control IGB from scripts, which are text files containing simple commands for navigation, loading data, and making snapshots.
To run an IGB script:
- Open a script file using File > Open. Script files should end with .igb.
- Click an IGB script link. See: Controlling IGB using IGB Links
- Drag and drop 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
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"genome <version>"
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Bring IGB to front
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bringToFront |
Bring the IGB window to the front of the user's desktop.
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Open a genome version
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genome <version>
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Open genome version (e.g., H_sapiens_Mar_2006). Any genome version or synonym that's accepted by IGB is accepted here.
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Go back to the IGB start screen.
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homescreen |
Return to the IGB start screen.
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Go to a region
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goto <region>
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Go to a region of a chromosome (e.g., "chr1:40000-60000" or "chr1:40,000-60,000"). Commas are optional. Any region format
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accepted by the IGB
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"load <file or URL>"quick search text entry (top left corner) is acceptable.
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Hide a track
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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
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load <file or URL>
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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.
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"loadmode
Remove a data set from IGB's list of active data sets
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unload <file or URL>
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Change the load mode for an active (opened) data set
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loadmode <NO_LOAD | REGION_IN_VIEW | CHROMOSOME | GENOME> <file or URL> |
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Change the load mode for the specified
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data set or file, identified by full path
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"refresh"
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.
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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
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refresh
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This is equivalent to clicking the Load Data button in IGB. This
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| Wiki Markup |
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"snapshot \[<filename>\]" or "snapshotwholeFrame \[<filename>\]" |
| Wiki Markup |
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"snapshotmainView \[<filename>\]" |
| Wiki Markup |
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"snapshotmainViewWithLabels \[<filename>\]" |
Wiki Markup
Make images
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snapshot <filename>
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| Code Block |
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snapshotwholeFrame <filename>
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| Code Block |
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snapshotmainView <filename>
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snapshotmainViewWithLabels <filename>
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snapshotslicedViewWithLabels <absolue path to file>
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Export the entire frame, main view, main view with labels, or sliced view, respectively, to a PNG format file.
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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.
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"select <geneids>"
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The snapshot and snapshotwholeFrame commands only work on Mac and Linux if attempting to export an SVG file. |
Select genes
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select <geneids>
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Selects the given gene IDs, which are passed in as a comma-separated
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list."sleep <milliseconds>"
Wait (sleep) for commands to finish
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sleep <milliseconds>
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Sleep the application for x milliseconds.
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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. |
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Example script
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#select genome genome |
Comments
Lines starting with the IGB script comment character '#' are ignored.
Examples
Loading a BAM file
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# select genome genome A_thaliana_Jun_2009 #go to chromosome at region goto chr4:18,040,000 - 18,045,056 #load the file load# go to a region in chr4 # commas are optional goto chr4:8,860,484-8,872,096 # load a file load http://bioviz igbquickload.org/quickload rnaseq/A_thaliana_Jun_2009/nextgen_samples SRP029896/sample ColdControl.bam #set load mode to region in view loadmode REGION_IN_VIEW http://bioviz.org/quickload/A_thaliana_Jun_2009/nextgen_samples/sample.bam #refresh to view data refresh
# load the data
refresh |