Commands | Arguments | Description | Examples |
---|---|---|---|
bringToFront | none | Make IGB the top window on the Desktop. | bringToFront |
genome | <version> | Load a genome version. Accepts IGB-friendly genome version names (e.g., H_sapiens_Feb_2014) and synonyms. | genome H_sapiens_Mar_2006 |
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 | CHROMOSOME | GENOME> <file or URL> | Change the load mode a data set. Ann's note: Check that the Data Management table changes the settings and that the loading of data changes as it should. | loadmode GENOME http://igbquickload.org/M_musculus_Dec_2011/M_musculus_Dec_2011_refGene.bed.gz |
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. Ann's note: doesn't work. Let's remove it. | select AT1G36280.2,AT1G36240.1,AT1G36340.1 |
selectfeature | <geneids> | Selects the given gene IDs, which are passed in as a comma-separated list. Ann's note: doesn't work. Let's remove it. | 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. Ann's note: doesn't work on Windows at all. Users has to specify the full path to the file. Using "~" to indicate HOME directory fails. If you don't give the full path, the file gets saved to ??? | 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. | 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. Ann's note: Removes the track but leaves it in the Data Management Table. | unload http://igbquickload.org/A_thaliana_Jun_2009/cold_stress/cold_control.sm.bam |