[Bioperl-l] Seq(IO) documentation thoughts

Ewan Birney birney@ebi.ac.uk
Mon, 18 Dec 2000 09:07:17 +0000 (GMT)

On Mon, 18 Dec 2000, Kris Boulez wrote:

> 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.

I think we should aim for complete round-trip information transfer. We
just haven't tested this area hard enough.

> 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.

$seqobj->trunc(10,50) does this.

> Kris,
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420