[BioRuby] Alignment plugin

Pjotr Prins pjotr.public14 at thebird.nl
Tue Apr 27 07:38:13 UTC 2010

Hi Peter,

On Mon, Apr 26, 2010 at 06:56:26PM +0100, Peter wrote:
> In these file format, am I right in thinking the non-sequence based
> characteristics are all still encoded by single letters? e.g. single
> digits. If so, that still allows the data to be held as simple strings.

Strings have an elegance to them - in particular because so much
built-in functionality of Ruby and Python allow for concise readable
code (like regular expressions).

However, there are short-comings. In particular where we aim for
testing correctness and adding annotations. I would rather have a
nucleotide as an object than as a string character.

I think we can have it both ways. But don't try to enforce a String
on something that is conceptually something else.

BTW The GSoC Perl alignment project has been approved and they are
also rethinking rather fundamental implementation details.

I don't intend to replace Bio::Sequence, but rather come up with a
parallel alternative. 


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