sequence quality in eprimer3

[Peter Rice]

Guy Bottu wrote:
> I am afraid that the EMBOSS "wrapper" program eprimer3 does not handle the base 
> assignment qualities, even if the manual briefly mentions it. Actually, EMBOSS 
> does not handle Staden experiment files. If you ask seqret to write 
> experiment::xxx it writes a sequence in the now obsolete Staden format.
> (let's not blame the developers, it is such a monumental task to implement 
> everything...)

Not too difficult. I believe the Staden experiment file format is 
similar to EMBL.

We don't see the Staden format as obsolete (and only GCG seem to call it 
"Staden" - it's just a nice name for a plain sequence format.

> You might install primer through its "native" interface, using the 
> primer3_www.cgi script. This is more rich than EMBOSS, but is of course 
> "featureless" (no access to personal files on the server). You still will have 
> to extract "manually" the content of the AV lines and copy-and-paste in the 
> "Sequence Quality" box.

We could try adding the base qualities - yet more options for eprimer3.

How many users would like this added in EMBOSS?

Peter