IGB User's Guide
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Comment: The URL in the code block in the Examples section was outdated, so that's now been updated.

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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

CommandsArgumentsDescriptionExamples

bringToFront

none

Make IGB the top window on the Desktop.

Code Block
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.
Code Block
genome <version>
goto<region>Go to a region. Any format that's accepted by IGB is accepted here. Commas are optional.
Code Block
goto chr1:13,640,211-13,643,760

goto chr1:13640211-13643760
hidetrack<file or URL>Hide the track. Accepts one or more comma separated files identified by full path or URL.
Code Block
hidetrack http://igbquickload.org/H_sapiens_Dec_2013/H_sapiens_Dec_2013_all_mrna.psl.gz

 

homescreennoneReturn to the IGB Start Screen.
Code Block
homescreen
load<file or URL>Load the specified file or URL into IGB. The data set will appear in the Data Management table upon completion. Note that if loading a file, the full path is required.
Code Block
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
loadsequencenoneThis is equivalent to clicking the Load Sequence button in IGB. This triggers loading of the reference sequence for the region in view.loadsequence
refreshnone

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.smSRP029896/ColdControl.bam
# load the data
refresh

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https://gist.github.com/Hillrunner2008/25976458488b65a3a25b

 

 

 

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