[Bioperl-l] {SPECS] Sequence meta data

[Peter Schattner]

First of all, thanks for taking this on, Heikki.  I think this will be
useful to a lot of people.

But...

Heikki Lehvaslaiho wrote:

>The idea is that meta data makes sense only in the context of the
>sequence and should be stored as an integral part of the sequence
>object.

This points up something in Bioperl that has been confusing me for a while
? what belongs in a Seq vs what belongs in a SeqFeature on that Seq?
Generally when I need to use "meta" sequence information it is associated
with a gene, a transcript or some other "feature" rather than an entire
sequence.  Consequently I have assocated metasequence information with
SeqFeature objects rather than Seq objects.  This also has the benefit that
I am able to write out these annotations using Bio::Tools::GFF.

Quality data is probably most appropriately associated with entire
sequences.  But encodings and other metasequence info seem to me are more
often be associated with a feature rather than the entire underlying
sequence. (I realize that Seq::Encoded associates metasequences with
sequences rather than features, but I’m not convinced this is desirable).

Well, I’m not adamant about this, but I think this will eventually affect
others and is worth a bit a thought before jumping totally into the idea
that metasequence information should always be connected to the Seq rather
than the SeqFeature.

My $0.02 worth.

Peter