showfeat overlaping CDS

[Peter Rice]

David Bauer wrote:

> I have a EMBL file with 2 CDS entries which stand for alternatively
> spliced products. I would like to display only one of them at a time
> with showfeat.
> Both have a /gene and /label with the gene name (e.g. gene1 gene2).
> So what I thought was to use:
> -matchtype=cds -matchtag=label -matchvalue=gene1
> The matchtype works as I expect but with any kind of matchtag or
> matchvalue I'm getting core dumps.

Works for me with 2.0.1, but purify complains horribly - most likely the
same problem. We will fix it and add these command line options to the new
test set.

> Also if I use -tags with a spliced CDS the tags are displayed only with
> the first exon, all other exons get just a CDS so it is not visible
> which of the remaining exons belongs to which of the genes.

Internally the tags are stored with the first exon. They include an
implicit group tag that can be displayed with the other exons. Is that what
you need?

If you print out a feature table in GFF format (with seqretallfeat) what
you see is pretty much what is stored internally. The Sequence and
FeatFlags information is part of the feature data, rather than part of the
tag-value list, and is used for keeping multiple exons together. For
example:

seqretallfeat tembl:hsegl1 gff::hsegl1.gff

We could probably add the Sequence tag to the showfeat output (although it
is not part of the EMBL feature table) or we could duplicate all the tags
if that's what users would prefer.

A short example from the test data set would be:

showfeat tembl:hsegl1 -tags


-- 
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Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723