Hi David. On 04/06/2014 18:33, David M Garcia wrote: > Is there a way I can extract the conservation values corresponding to > one of the other proteins in the alignment? I would like to be able to > extract conservation scores for the residues only present in certain > proteins in my alignment (in an excel friendly format), without all > the gaps. I've lodged a feature request about this (http://issues.jalview.org/browse/JAL-1516). I also came up with a fairly messy script that might do what you need:
Open Jalview's groovy console (http://www.jalview.org/help/html/features/groovy.html) and paste in the following: // very messy script to output the scores in annotation rows for the first sequence in a selection on the topmost alignment def curviewport = Jalview.getAlignframes()[Jalview.getAlignframes().length-1].getViewport(); if (curviewport.getSelectionGroup()) { // gets selection for 'first' alignment - note this is the 'oldest' one - can't access the current alignment as yet def selreg = curviewport.getSelectionGroup(); def gaps = selreg.getSequenceAt(0).gapMap(); // aligned positions of first sequence selected String csvfile=""; curviewport.getAlignment().getAlignmentAnnotation().eachWithIndex{ aa, apos -> String csv="" gaps.eachWithIndex{col,spos -> if (col>=selreg.getStartRes() && col<=selreg.getEndRes()) { // output height of histogram csv+=","+aa.annotations[col].value; // Uncomment to output string shown in tooltip // csv+=","+aa.annotations[col].description; }} if (csv.length()>0) { csvfile+=aa.label+csv+"\n" } } print csvfile; } else { "Select a region in the alignment window."; } /// Hope that helps! Jim ps. You can also find this script in a comment on the feature request: http://issues.jalview.org/browse/JAL-1516?focusedCommentId=13296&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-13296 _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
