Hi Jens - I’ll answer your question first… and then comment on the first part of your email…
I tried for quite some time, but I failed already at the step to get a group logo from an annotation file. Is there a way to do this?
There ought to be, but looking at the AnnotationsFile documentation (http://www.jalview.org/help/html/features/annotationsFormat.html) I see there actually isn’t a formally defined mechanism.
There is a workaround - simply specify a .jalview_properties file (via -props) that contains ‘SHOW_GROUP_CONSENSUS=true’ (and at least one newline afterwards), and group consensus will be shown.
Thanks for your great tool. I am trying to do a batch analysis for several alignments, thus I need the command line. I would like to define a group and to show the consensus logo of this group, but not the logo of the complete alignment. Then I want to hide this group, define the consensus sequence as reference and show the differences to the reference in the remaining sequences.
OK. It sounds to me as if you are passing a Groovy script to Jalview to perform these operations. is that the case ? Otherwise, if you are simply aiming to generate figures, you can only do one of these two steps via the command line! (ie you cannot pass a sequence of commands like -openFile … -png …more commands… -png outfile).
If you are happy to launch Jalview multiple times, then you simply need to pass another custom properties file containing ‘SHOW_UNCONSERVED=true’ to show differences w.r.t. the consensus (ie - you don’t need to specify a reference sequence, since default behaviour is to show differences w.r.t Jalview’s consensus).
Creating a groovy script to do all this would also be possible, but I’ve not tried so I’m not sure how complex it will be …
Hope this helps!
Jim.
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On 09/11/2017 18:28, Jens Georg wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)