sequence quality in eprimer3

[Peter Rice]

Guy Bottu wrote:
>>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.

Extra line types are easy to ignore.

We would need some example files (to be saved in the test/data 
directory) to QA test the code.

>>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 format is obsolete and the programs do not write or read it anymore.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".

"experiment" is another name for "staden". Easiest is probably to make 
it another name for "embl" if we can handle the format differences. Or 
we can make a copy of the ReadEmbl functions and make the expriment 
format changes there.

>>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.

eprimer3 certainly needs lots of sections. Suggestions for good ways to 
split the sections are welcome (they only apply to GUIs - EMBOSS will 
ignore them anyway).

All we need are:

section
   section
     list of ACD qualifiers
   endsection
endsection