An IGB script file is a simple batch file that allows a user to run sequential commands outside of IGB, either at startup (via a command-line option) or during the run (via a URL "Bookmark" option -- see control bookmark). It can also be loaded via the File->Load menu (or via drag-and-drop) if its filename extension is ".igb".
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Introduction
You can control IGB from scripts, which are 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.
Syntax
The script file has a simple, space-delimited syntax.
Options
"genome <version>"
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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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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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Go back to the IGB start screen.
| Code Block |
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homescreen |
Return to the IGB start screen.
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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" or "chr1:40,000-60,000"). Commas are optional. Any region format
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accepted by the IGB
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"load <file or URL>"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
| 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.
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"loadmode
Remove a data set from IGB's list of active data sets
| Code Block |
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unload <file or URL>
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Change the load mode for an active (opened) data set
| Code Block |
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loadmode <NO_LOAD |
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| REGION_IN_VIEW | CHROMOSOME | GENOME> <file or URL>
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Change the load mode for the specified
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data set or file, identified by full path
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"refresh"
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.
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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
| Code Block |
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refresh
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This is equivalent to clicking the Load Data button in IGB. This
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| Wiki Markup |
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"snapshot \[<filename>\]" or "snapshotwholeFrame \[<filename>\]" |
| Wiki Markup |
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"snapshotmainView \[<filename>\]" |
| Wiki Markup |
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"snapshotmainViewWithLabels \[<filename>\]" |
Wiki Markup
Make images
| Code Block |
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snapshot <filename>
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| Code Block |
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snapshotwholeFrame <filename>
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| Code Block |
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snapshotmainView <filename>
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| Code Block |
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snapshotmainViewWithLabels <filename>
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| Code Block |
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snapshotslicedViewWithLabels <absolue path to file>
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Export the entire frame, main view, main view with labels, or sliced view, respectively, to a PNG format file.
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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.
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"select <geneids>"
| Info |
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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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Selects the given gene IDs, which are passed in as a comma-separated format.
"sleep <milliseconds>"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.
Example script
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| Note |
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
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# select genome genome A_thaliana_Jun_2009 goto chr4:18,040,000 - 18,045,056 load# go to a region in chr4 # commas are optional goto chr4:8,860,484-8,872,096 # load a file load http://bioviz igbquickload.org/quickload rnaseq/A_thaliana_Jun_2009/nextgen_samples SRP029896/sample ColdControl.bamloadmode VISIBLE http
# load the data
refresh |
Exporting images
https://
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gist.github.
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com/
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