Bioperl-guts: seq reimplementation

James Gilbert jgrg@sanger.ac.uk
Mon, 16 Aug 1999 13:47:31 +0100 (BST)



Ewan,

Final proposal looks good to me.  I look forward
to a nice warm fuzzy feeling when I use the new
objects.

On your two unresolved isssues:

- case of sequence characters (so petty! and yet
  so important!)

I think it should just keep the case of the
sequence it gets.  Performance will be worse where
case-insensitve matches are used, but I think this
will avoid a lot of uppercasing and lowercasing in
users scripts.

- alphabet paranoia

Could be taken care of in subclasses of Bio::Seq,
when setting the sequence string, so it can be
used if wanted:

	Bio::Seq::DNA
	Bio::Seq::RNA
	Bio::Seq::Amino (which makes revcom fatal)

James

On Sat, 14 Aug 1999, Ewan Birney wrote:

> 
> A final proposal is up at
> 
> http://bio.perl.org/Projects/Sequence/reimpl.html
> 
> I am going to start to get to work on the basis of this proposal,
> assumming that people are ok with it (and only minor changes).
> Notice I need some ideas about
> 
> 	- case of sequence characters (so petty! and yet so important!)
> 
> 	- alphabet paranoia
> 
> I have encorporated many ideas given to me about this. Notice
> the backward compatibility functions which throw warnings, and
> the lack of translate but a descriptive error message.
> 
> 
> 
> 
> 
> Ewan Birney
> <birney@sanger.ac.uk>
> http://www.sanger.ac.uk/Users/birney/
> 
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James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919

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