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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.
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Supported commands
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genome <version>
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- Specify a 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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goto <region>
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- Go to a region of a chromosome (e.g., "chr1:40000-60000"). Any format that's accepted by IGB is accepted here.
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load <file or URL>
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- Load the specified file (identified by full path) or URL into IGB.
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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 feature (identified by full path).
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refresh
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- 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
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snapshot \[<filename>\] |
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snapshotwholeFrame \[<filename>\] |
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snapshotmainView \[<filename>\] |
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snapshotmainViewWithLabels \[<filename>\] |
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snapshotslicedViewWithLabels \[<filename>\] |
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- 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.
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select <geneids>
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- Selects the given gene IDs, which are passed in as a comma-separated list.
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sleep <milliseconds>
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- Sleep the application for x milliseconds.
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#
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Comment
- Comments. Lines starting with '#' are ignored.
Example script
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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 http://igbquickload.org/quickload/A_thaliana_Jun_2009/nextgen_samples/sample.bam #set load mode to region in view loadmode REGION_IN_VIEW http://igbquickload.org/quickload/A_thaliana_Jun_2009/nextgen_samples/sample.bam #refresh to view data refresh |