Hi Jim.. Great to be back on jalview discuss. Am looking at a lot of alignments these days and loving the new features in Jalview ( esp the super easy map to structure , secondary structure predicition etc)
Thanks for speedy reply. I was able to get the column residue positions ..by a two step process following your hint 1) Creating a feature by selecting the columns containing the start and stop boundaries--Selection(rigthclick )- Create sequence feature 2) Then ..going to File in main menu and outputting the feature to a file. 3) That file then contains a csv of feature name and start and stop boundaries I have another question about Selection output to a FASTA file. In earlier versions the selection would have the start and stop residues of the selection annotated in the fasta file..and not start and stop of the whole sequence: any ideas how to get the old style output. Since this is a separate issue I will ask a separate question here.. Thanks again Hari On Fri, Sep 12, 2014 at 6:03 AM, Jim Procter <[email protected]> wrote: > 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 >
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