Introduction
You can control IGB from scripts, text files containing simple commands for navigation, loading data, and making snapshots.
To run an IGB script:
- 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. | genome <version> |
| 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
|
| 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 |
Open a genome version
genome <version>
Open genome version (e.g., H_sapiens_Mar_2006). Any genome version or synonym that's accepted by IGB is accepted here.
Go back to the IGB start screen.
homescreen
Return to the IGB start screen.
Go to a region
goto <region>
Go to a region of a chromosome (e.g., "chr1:40000-60000" or "chr1:40,000-60,000").
Add a new data set to IGB's list of active data sets
load <file or URL>
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.
Remove a data set from IGB's list of active data sets
unload <file or URL>
Change the load mode for an active (opened) data set
loadmode <NO_LOAD | REGION_IN_VIEW | CHROMOSOME | GENOME> <file or URL>
Change the load mode for the specified data set or file, identified by full path.
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
refresh
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.
Make images
snapshot <filename>
snapshotwholeFrame <filename>
snapshotmainView <filename>
snapshotmainViewWithLabels <filename>
snapshotslicedViewWithLabels <absolue path to file>
Export the entire frame, main view, main view with labels, or sliced view, respectively, to a PNG format file. You must include the full path to the file or IGB will write the file to the location from where you launched IGB.
The filename defaults to "<genome_version><timestamp>.png" if not specified.
The snapshot and snapshotwholeFrame commands only work on Mac and Linux if attempting to export an SVG file.
Select genes
select <geneids>
Selects the given gene IDs, which are passed in as a comma-separated list.
Wait (sleep) for commands to finish
sleep <milliseconds>
Sleep the application for x milliseconds.
IGB is multi-threaded, which means that the user may be able to operate IGB while data are being loaded. If your IGB script includes loading data from remote sites (e.g, RNASeq data from the IGBQuickLoad.org site) then you should include a sleep command to give IGB time to load the data.
Comments
Lines starting with the IGB script comment character '#' are ignored.
Examples
Loading a BAM file
# 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 # load the data refresh
Exporting images
https://gist.github.com/Hillrunner2008/25976458488b65a3a25b