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You can control IGB from scripts, which are text files containing simple commands for navigation, loading data, and making snapshots.
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- 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.
Commands
| Commands | Arguments | Description | Examples | ||
|---|---|---|---|---|---|
bringToFront | none | Make IGB the top window on the Desktop. | bringToFront | ||
| genome | <version> | 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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| goto | <region> | Go to a region. Any format that's accepted by IGB is accepted here. Commas are optional. | goto chr1:13,640,211-13,643,760 goto chr1:13640211-13643760
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| hidetrack | <file or URL> | Hide the track. Accepts one or more comma separated files identified by full path or URL. | hidetrack http://igbquickload.org/H_sapiens_Dec_2013/H_sapiens_Dec_2013_all_mrna.psl.gz | ||
| homescreen | none | Return to the IGB Start Screen. | homescreen | ||
| load | <file or URL> | Load the specified file (identified by full path) or URL into IGB. The data set will appear in the Data Management table upon completion. | load http://igbquickload.org/D_melanogaster_Jul_2014/D_melanogaster_Jul_2014.bed.gz | ||
| loadmode | <NO_LOAD | REGION_IN_VIEW | GENOME> <file or URL> | Change the load mode for a data set. Note: The loadmode command will work for any loaded track. Make sure to load your desired track before calling the loadmode command. | loadmode GENOME http://igbquickload.org/M_musculus_Dec_2011/M_musculus_Dec_2011_refGene.bed.gz | ||
| loadsequence | none | This is equivalent to clicking the Load Sequence button in IGB. This triggers loading of the reference sequence for the region in view. | loadsequence | ||
| refresh | none | 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. | refresh | ||
| select | <geneids> | Selects the given gene IDs, which are passed in as a comma-separated list. If the command contains a single gene ID then IGB will select and jump-zoom to the given gene. | select AT1G36280.2,AT1G36240.1,AT1G36340.1 | ||
| selectfeature | <geneids> | Selects the given gene IDs, which are passed in as a comma-separated list. | selectfeature | ||
| showtrack | <file or URL> | Unhide the specified track. Accepts one or more comma separated files identified by full path or URL. | showtrack http://igbquickload.org/O_sativa_japonica_Oct_2011/O_sativa_japonica_Oct_2011.bed.gz | ||
| sleep | <milliseconds> | Sleep the application for x milliseconds. | sleep 6000 | ||
| snapshot | <filename> Note: specify the full path to file. | Create an image showing the entire IGB window. the entire frame an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg. Note: This command only works on Mac and Linux if attempting to export an SVG file. | snapshot alternativesplicing1.png | ||
| snapshotmainView | <filename> | Same as snapshot but only makes an image showing the main IGB data display. | snapshotmainView testimage.jpeg | ||
| snapshotmainViewWithLabels | <filename> | Export the main view with labels an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg. | snapshotmainViewWithLabels imageexport1.svg | ||
| snapshotslicedViewWithLabels | <filename> | Export the sliced view an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg. | snapshotslicedViewWithLabels April_1_2015.png | ||
| snapshotwholeFrame | <filename> | Export the entire frame to an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg. Note: This command only works on Mac and Linux if attempting to export an SVG file. | snapshotwholeFrame GeneAT1G36280wholeframe.jpeg | ||
| unload | <file or URL> | If a matching track is found for the specified URL/path it will be deleted. Accepts one or more comma separated files identified by full path or URL. | unload http://igbquickload.org/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bam |
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.
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Open a genome version
| Code Block |
|---|
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 |
|---|
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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| 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.sm.SRP029896/ColdControl.bam # load the data refresh |
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https://gist.github.com/Hillrunner2008/25976458488b65a3a25b
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