Hello Hari - great to hear from you :) On 12/09/2014 03:14, hari jayaram wrote: > I was wondering if there is a way to get all the residue positions for > a particular selected column in an alignment
There isn't a way to get the positions exactly as you want. You could manually get positions by selecting just one column and exporting the region to an alignment file (right click and follow the selection submenu), but that's pretty cumbersome if you need to do it for more than a couple of columns. I've asked our new Jalview developer, Mungo Carstairs, to take a look at this, since it should be fairly straightforward to put together a groovy script to do what you want. > I have 83 sequences in an alignment, I select a particular column , by > clikcing on top ,and get the red bar. After this I can mouse over each > sequence and see the residue numbers in the bottom. > So the output would look like > > gi 12134567 833, P > gi 23456789 782 P > gi 12456789 830 P > gi 32737237 - - > > ....and so on for all 83 sequences more sequences I created a JIRA issue so we can discuss the fine details (http://issues.jalview.org/browse/JAL-1542). For the moment, we were wondering if you wanted to export the positions for a number of columns ? e.g. for a range of columns highlighted with red column marks output: # Alignment column 1 gi 12134567 833 P gi 23456789 782 P gi 12456789 830 P gi 32737237 - - # Alignment column 5 .. Is that the kind of thing you'd need ? Jim. _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
