[Bioperl-l] Seq(IO) documentation thoughts

[Kris Boulez]

Over the weekend I've been writing some example code (for the seq/seqio
part of BioPerl). The pratical issues I encountered I'll save for my
answer to Peter's mail.

One thing I want to ask here. How far do we want to go in having BioPerl
(SeqIO) being a format convertor ? I've played around a bit with
converting one sequence formati (a) to another (b) and using (b) as
input for another round. It turns out that after some rounds (mostly <10)
BioPerl isn't -w clean anymore ('use of uninitialized value ...') or
just throws an error. Is it worth investigating this, or do we just say
that we only support one conversion.

Something else I noted, that we'll have to explain well in the
docs is the difference between Seq (the sequence object) and ->seq()
(the sequence as  a string). People might want to expect that
$seqobj->subseq(10,50) returns a new sequence object and not the string.
Would such a method make sense.

Kris,