Bio::Seq (was:Robert's chapter :))

[Georg Fuellen]

Hi Chris,

Thanks a lot for playing around w/ Bio::Seq !
Did you not find any bugs ? (Wondering .. :-)
I'll try to briefly comment on the code today/tomorrow.

Do you think you could prepare Bio::Seq for a first beta release until, say,
Dec 15 (and Steve Brenner and/or I would do some final checking) ?
That would include:
+ completing the POD (search for ``to be completed'' in Seq.pm)
+ add code to testSeq.pm testing/demonstrating your new code in particular
+ alphabet checking (before storing sequences in the object hash)
+ integrate Gilbert's ReadSeq so that it's called as a command for
  converting exotic formats, _if_ it's installed (before calling
  parse_bad )

The beta release should not yet be announced to bioperl@mole,
only to vsns-bcd-perl and those ppl who agreed to beta-test.
Especially, we want to fix parse_unknown before going public.
I've been told repeatedly that parse_unknown
is standard, parseUnknown isn't good, do you agree ?)

>  Georg,
> 
> In you previous reply you asked me to "check w/ Robert's chapter (appendix)"
> regarding nucleotide symbols and ambiguity codes. I'm not quite sure what
> document(s) you were refering to.

I meant
http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/prwali.html
and 
http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/node7.html#SECTION00072000000000000000
(``6.2 The extended genetic alphabet'') in particular.

I'm very thankful to have you on board :)
georg

> Regards,
> Chris Dagdigian
> 
> 
>