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Introduction
Starting with IGB 6.3, IGB supports a simple scripting language that contains commands related to loading data from files and URLs.
Scripts can be run
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you can control IGB from scripts, text files containing simple commands for navigation, loading data, and making snapshots.
You can run an IGB script:
- By opening a script file using File > Open. Script files should end with .igb or .js for javascript; with plug-in IGB will also accept .py for python).
- From IGB links. See: Controlling IGB using IGB Links
- By drag-and-drop, dragging the file into an open IGB window
Note: A protoype plug-in enabling python scripts (.py extension) was developed but is not yet released. If you would like to know more, please get in touch.
Syntax
The script file has a simple, space-delimited syntax. Each command should occupy a separate line.
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Specify a genome version
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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.
Go to a region
| Code Block |
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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.
Add a new data set to IGB's list of active data sets.
| Code Block |
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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.
Change the load mode for an active (opened) data set.
| Code Block |
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loadmode <NO_LOAD | REGION_IN_VIEW | CHROMOSOME | GENOME> <file or URL>
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Load data from currently active data sets.
| Code Block |
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refresh
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This is equivalent to clicking the Load Data button in IGB. This triggers loading of data from the active data sets available in IGB, as specified in the load command.
Making images
| Code Block |
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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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Supported formats are those supported by IGB Export function. The filename defaults to "<genome_version><timestamp>.png" if not specified.
Select genes.
| Code Block |
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select <geneids>
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Selects the given gene IDs, which are passed in as a comma-separated list.
Wait (sleep) for commands to finish
| Code Block |
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sleep <milliseconds>
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Sleep the application for x milliseconds.
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Lines starting with the IGB script comment character '#' are ignored.
Example script
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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/quickload/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bam # set load mode to region in view loadmode REGION_IN_VIEW http://igbquickload.org/quickload/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bam # load the data refresh |