[Bioperl-l] Seq(IO) documentation thoughts

Hilmar Lapp hlapp@gmx.net
Mon, 18 Dec 2000 02:08:03 -0800

Kris Boulez wrote:
> 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.

We had a similar discussion some months ago. Quoting myself :O) from

--- quote on
The point I'd like to make may be best illustrated by comparing with
automated language translators that are around (like babelfish;
babelfish.altavista.com). Try to translate an only slightly complicated
sentence from one language into another, which already screws it up
half-way, and then translate the result into a third. I think it is
pointless for BioPerl to aim at clean and complete conversion from any
rich format into another rich format for sequences.

The only way this could be achieved with a reasonable effort is by
mapping languages to a common meta-representation, like XML or ASN.1
anything the meta-format doesn't cover will still be lost).
--- quote off

This more or less was approved consensus, at least to my humble
understanding. I can easily imagine that there are still parsing bugs
making things worse, and these obviously need to be eliminated.


Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757