Automate jalview to generate wrapped alignment figure

Jalview Discussion
1

Hi,

I am trying to visualize more than 1000 MSA alignments and generate png image using jalview. I can automate so that jalview generate alignment figures for all the MSA alignments. But, in the result figures, the full sequence in a single line (more than 1000 amino acids). It seems very difficult analyze or present those figures. Is there any option to wrap the alignment in the figure or mention how many amino acids should appear in a line?

Also, how to mention “clustal” color and “label above”

Thanks

2

Hi @Naga

I’m assuming you are using Jalview 2.11.3 - in which case the following will work:

jalview --open="*.fa" --colour clustal --wrap --image="{basename}_output.png" --close --headless --substitutions

I’ve just tested this with the jalview package from conda on OSX. You may find there are problems if your sequence IDs are very long - we have a patch ready to ship in the next bug-fix release, due next week(ish), but already available in Jalview Test. If you have java installed just download the executable Jar and run it via java -jar <executable jar> [jalview arguments]

3

One more thing – I reread your post and realised I’m not quite sure what you meant by:

Practically all of Jalview’s interactive controls for MSA visualisation can be specified on the command line - let us know what you mean and we’ll try and help !
Jim.

4

Hi,

Thanks you your details. I am trying the following command

./Jalview --open=folder_name/*.fasta --colour clustal --all --wrap --image=folder_name/{basename}.png --close --headless --substitutions --noshowannotations

This command successfully generating png images for upto 160 alignments. Afterthat, it was showing the following error before terminating. Any idea how to solve this issue and to generate png files automatically for all the files

"Exception in thread “main” java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextNode(HashMap.java:1469)
at java.util.HashMap$KeyIterator.next(HashMap.java:1493)
at java.util.AbstractCollection.toArray(AbstractCollection.java:196)
at jalview.workers.AlignCalcManager.getRegisteredWorkersOfClass(AlignCalcManager.java:313)
at jalview.viewmodel.AlignmentViewport.updateConservation(AlignmentViewport.java:840)
at jalview.viewmodel.AlignmentViewport.alignmentChanged(AlignmentViewport.java:1884)
at jalview.gui.AlignmentPanel.alignmentChanged(AlignmentPanel.java:214)
at jalview.gui.AlignFrame.setAnnotationsVisibility(AlignFrame.java:5858)
at jalview.bin.Commands.showOrHideAnnotations(Commands.java:918)
at jalview.bin.Commands.processLinked(Commands.java:857)
at jalview.bin.Commands.processArgs(Commands.java:131)
at jalview.bin.Jalview.doMain(Jalview.java:841)
at jalview.bin.Jalview.main(Jalview.java:258)
"

Thanks

5

Hi - the forum’s email was not working so we missed your reply. Very sorry about that !

You’ve definitely found a bug - we’ll have a go at reproducing it, but I guess you’ve found a workaround for this just now.

A thousand apologies !