sequence quality in eprimer3

[Guy Bottu]

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

Already now EMBOSS can read in sequences in "experiment" format, because it 
takes it for EMBL format. There is however a problem : in experiment format the 
SQ
  ACGT...
//
does not necessarily come at the end of the file ! Also, there are a lot of 
extra tags. Maybe some of them, like the AV lines, need some special treatment 
in EMBOSS.
 
> 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).

Well, the manual of the last version of the Staden package mentions that the 
format is obsolete and the programs do not write or read it anymore.
If I am not wrong, Staden format differs in two things from "raw" format :
- it allows for embedded comments between <> at any place in the sequence 
(EMBOSS writes and reads staden:xxx files with a comment at the top, but does 
not allow comments anywhere else)
- traditionally Staden used for ambiguous bases the Stanford-Staden codes rather 
than the IUPAC-IUB (but they seem to have abandonned this)

I think EMBOSS should certainly support "experiment" format. There is no problem 
with continuing to support also "staden", but then maybe do it correctly and not 
confuse it with "experiment" or "rax"/"text"/"plain".

> We could try adding the base qualities - yet more options for eprimer3.
> 
> How many users would like this added in EMBOSS?

I have no idea how many users want to access all the options of Primer. It can 
certainly do no harm to support them all. But maybe then split the page in more 
"type:page" sections. In Staden, eprimer3 is unusable because the "Start" button 
disappears below the bottom of the screen. I do not know if other GUI's also 
have problems.

	Guy Bottu