Seems my script got a bit truncated - here it is again:
/// groovy script for inserting taxon name at beginning of sequence ID
import jalview.datamodel.*;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
// matches the species name in [parentheses]
def descpattern = ~/.*\[([^]]+)/;
def af = Jalview.getAlignframes();
// walk through all alignments, processing all sequences
for (ala in af)
{
def al = ala.viewport.alignment;
if (al!=null)
{
SequenceI[] seqs = al.getSequencesArray();
for (sq in seqs)
{
if (sq!=null) {
if (sq.getDatasetSequence()!=null)
{
// extract species from dataset sequence description
// and place at beginning of ID string in alignment
def mtch = (
sq.getDatasetSequence().getDescription().replaceAll(descpattern,'$1')
+"|"+sq.getDatasetSequence().getName());
sq.setName(mtch);
}
}
}
}
ala.repaint()
}
/// end of script - open Tools->Groovy console and paste this in
On 21/07/2014 10:36, Dr JB Procter wrote:
> Hello Deepak - this is a great suggestion !
>
> I've been meaning to introduce 'real' support for taxonomic names in
> Jalview for some time, but there always seemed to be something else that
> took higher priority. However - we will definitely have support for this
> in the next major Jalview release, and I'll do what I can to introduce
> basic support for this even sooner.
>
> For the moment, you could consider running this groovy script (via the
> groovy console under the tools menu) - which will do a search and
> replace to put anything in parenthesis at the beginning of the sequence
> name:
>
> /// groovy script for inserting taxon name at beginning of sequence ID
> import jalview.datamodel.*;
> import jalview.gui.AlignFrame;
> import jalview.gui.AlignViewport;
>
> // matches the species name in [parentheses]
>
> def descpattern = ~/.*\[([^]]+)/;
>
> def af = Jalview.getAlignframes();
>
> // walk through all alignments, processing all sequences
>
> for (ala in af)
> {
> def al = ala.viewport.alignment;
> if (al!=null)
> {
> SequenceI[] seqs = al.getSequencesArray();
> for (sq in seqs)
> {
> if (sq!=null) {
> if (sq.getDatasetSequence()!=null)
> {
> // extract species from dataset sequence description
> and place at beginning of ID string in alignment
> def mtch =
> sq.getDatasetSequence().getDescription().replaceAll(descpattern,'$1')
> +"|"+sq.getDatasetSequence().getName();
> sq.setName(mtch);
> }
> }
> }
> }
> ala.repaint()
> }
>
> /// end of script - open Tools->Groovy console, copy and paste into
> panel and hit the run button!
>
> It's a bit rough and ready, but should do what you want for the moment.
>
> hope that helps!
> Jim.
>
>
> On 18/07/2014 18:17, Deepak Barnabas wrote:
>> Dear Jim,
>>
>> Jalview is indispensable to the vast majority of structural biologists
>> including myself. Thanks for your good work with Jalview! We use it on an
>> everyday basis. I have a small suggestion. You probably already have this
>> option somewhere, and I am not looking hard enough. When visualising
>> multiple alignments, it would be very helpful if the organism name is
>> displayed instead of sequence name. Considering that a FASTA format download
>> of multiple sequences following a BLAST from NCBI always results in the
>> organism name being present in the sequence description within parentheses,
>> would it not be easy (as an option) if Jalview extracted the string within
>> these parentheses and displayed them instead of sequence name. Currently,
>> one has to individually hover over each sequence name to display its
>> description to look for the organism. Let me know, if I'm missing out on
>> something.
>>
>> Thanks!
>> Deepak
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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