Hello Amir. I've cced this to the Jalview discussion list - since that's where
you'd normally discuss feature requests like this.
On 29/04/2014 17:08, Geoff Barton wrote:
I am new Jalview user. I load my feature to my sequences by Jalview. Then I
aligned them. How can I export my feature from aligned file. I mean I need to
have new position of each animo acids in aligned file. Is it possible? If not,
Please help me how can I do that with other software or programming language?
This isn't something that is built in to Jalview, because we've never needed to
do this for our own analyses. However, it is very easy to do with a bit of
scripting.
If you open the Groovy console (from the tools menu), you can copy and paste in
the following script into the window that opens:
// start script
for (aw in Jalview.getAlignframes())
{
println("Aligned positions for features in alignment "+aw.getTitle());
for (sq in aw.getViewport().getAlignment().getSequences())
{
for (sf in sq.getDatasetSequence().getSequenceFeatures())
{
println([sf.getType(),sf.getDescription(), sq.findIndex(sf.getBegin()),
sq.findIndex(sf.getEnd())].join("\t")+"\n")
}
}
}
// end script
Then, hit the Run icon (or press control+R or CMD+R if you are on a mac) and
the output panel will contain the aligned positions for all the alignment
windows currently displayed in the Jalview desktop.
Is that what you were wanting to do ?
Jim
The University of Dundee is a registered Scottish Charity, No: SC015096
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