[Jalview-discuss] Jalview Discussion List / Jalview Sequence Feature File

Geoff Barton g.j.barton at dundee.ac.uk
Tue Feb 8 11:04:12 GMT 2011


Dear Iga,
Thanks for your feedback and particularly for pointing out the jalview 
discussion list was broken. I think Jim has now answered your specific 
jalview question and the list is now fixed!!
Thanks again,
Geoff.

On 05/02/2011 17:29, Iga Korneta wrote:
> Dear Professor Barton,
>
> The Jalview Discussion Mailing List subscription web page doesn't 
> work, so I'm not sure if the mailing list itself is working. This is 
> why I'm writing to you - no other contact has been given.
>
> I had a problem with the Jalview Sequence Feature File. I am running 
> Vista and Jalview 2.6.1.. I had annotations of secondary structure for 
> all sequences in the alignment from an external source. I used a 
> Python script to convert these to a sequence feature file which looked 
> just like in your documentation. This SFF didn't work, as in: upon 
> loading onto an alignment, it loaded into the alignment (new lines 
> were added to the alignment instead of colouring the alignment).
>
> I created some features in Jalview, exported these to a file, and 
> cut-and-pasted features (both colours and the features) from my file 
> into the Jalview-created file. This worked.
>
> I am happy that my solution worked. But could someone from your group 
> please explain what happened? I'm not sure if it's going to work next 
> time.
>
> Is it because of the additional carriage marks/line end marks in 
> Windows as opposed to Linux/Unix? Jalview has some trouble with them 
> in other places, too, I have noticed.
>
> With best regards,
> Iga Korneta

-- 
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          g.j.barton at dundee.ac.uk
Tel:+44 1382 385860/388731 (Fax:385764)     www.compbio.dundee.ac.uk

The University of Dundee is registered Scottish charity: No.SC015096




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