Hi All,
When I have a whole sub section of an alignment selected.Then I go to Selection–Output to Textbox- Fasta.
The resulting Fasta file has the sequence start stop feature for the whole sequence and not for the selected region.
So for example If I selected a region 60-80 of a giant alignment with sequences of different lenghts. Previously in Jalview I would have the output say
seq1| gi 123456 60-80
AGSGA-GAGGGA…
seq1 | gi 1244565 66-86
AGSGA-GAGGGA
But now the output says
seq1| gi 123456 1-887
AGSGA-GAGGGA
seq1 | gi 1244565 1-1021
AGSGA-GAGGGA
Any ideas how I can get the Fasta output to have the start stop for the selection. Or maybe I need to use a group and output to a new alignment?
What I want is to realign a sub-section of an alignment in a new Jalview window and preserve the residue numbers
Sorry I dont know how to accomplish this.
Thanks
Hari
Hi again Hari - I'm just starting to understand what you're aiming to do now 
When I have a whole sub section of an alignment selected.Then I go to Selection--Output to Textbox- Fasta.
The resulting Fasta file has the sequence start stop feature for the whole sequence and not for the selected region.
hmm. That's a bug (http://issues.jalview.org/browse/JAL-1486) that I haven't quite worked out how to elegantly fix do to some technical wrinkles in the way the parser is called.
Any ideas how I can get the Fasta output to have the start stop for the selection. Or maybe I need to use a group and output to a new alignment?
it's probably easiest if we just fix the bug in the 'next release' branch. It's already scheduled anyhow!
What I want is to realign a sub-section of an alignment in a new Jalview window and preserve the residue numbers
hmm. You could just select the region, copy and then paste to a new window - that will preserve numbering. You could also simply hide the regions you don't want to align, and then align the visible portion. Jalview will preserve the hidden columns in the new alignment so you keep the context.
Jim.
···
On 12/09/2014 12:54, hari jayaram wrote:
I've checked in a patch for the selected region->output to textbox bug - now available on the 'next release' build. There are still some minor issues which I'll tidy up over the weekend, but it should do what you need at the moment.
Jim.
···
On 12/09/2014 12:54, hari jayaram wrote:
Any ideas how I can get the Fasta output to have the start stop for
the selection. Or maybe I need to use a group and output to a new
alignment?
Thanks for your help Jim.
I could get a log of what I wanted done by selecting and realigning subsections of the alignment…that said I will await the next release build to have the output fasta have the correct register.
thanks again
···
On Friday, September 12, 2014, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
On 12/09/2014 12:54, hari jayaram wrote:
Any ideas how I can get the Fasta output to have the start stop for
the selection. Or maybe I need to use a group and output to a new
alignment?
I’ve checked in a patch for the selected region->output to textbox bug -
now available on the ‘next release’ build. There are still some minor
issues which I’ll tidy up over the weekend, but it should do what you
need at the moment.
Jim.
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