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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
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Syntax
The script file has a simple, space-delimited syntax. Each command should occupy a separate line.
Commands
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
| Code Block |
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genome <version> |
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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 accepted by the IGB quick search text entry (top left corner) is acceptable.
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Hide a track
| Code Block |
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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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Change the load mode for the specified data set or file, identified by full path.
| Info |
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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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The filename defaults to "<genome_version><timestamp>.png" if not specified.
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The snapshot and snapshotwholeFrame commands only work on Mac and Linux if attempting to export an SVG file. |
Select genes
| Code Block |
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select <geneids> |
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Lines starting with the IGB script comment character '#' are ignored.
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Examples
Loading a BAM file
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# 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 |
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