[Genquire-dev] coding a new adaptor layer from scratch

[Mark Wilkinson]

Mark Wilkinson wrote:

> The clock starts!
>
> I am going to try to code a Genbank flat-file adaptor layer from scratch...
> starting.... NOW!

Stop the clock :-)

Okay, I have a read-only genbank flat-file adaptor layer pretty much up and
working.  I had to figure out a few things as I went along, and I will update
the documentation with my experiences to make it easier for others in the
future, but I am guessing that it took at most 6-7 hours to put it together,
and would have been *considerably* faster if I had access to the several pages
of comments that are now on my desk!  On the other hand, I had the advantage
that I was working with a single "contig" in the Genbank file, and I had
BioPerl to parse the flat file in the first place.  It might not be *quite* so
easy under other circumstances.  Still - this shows that it really can be
done, and moreover can be done sufficiently quickly that, given a couple of
person-days investment, Genquire really could sit on top of any database!
Well done Dave!!!!!!

Before I commit this new adaptor layer to the CVS, along with some very minor
changes to Dave's Feature hierarchy (mainly comments to clarify some of the
more peculiar bits of code), I want to see how difficult it would be to make
it read/write and update some of the documentation in the Genquire adaptor
layer itself.

Anyway... Kudo's to Dave for putting together a reasonably straightforward
adaptof layer for Genquire :-)

M


--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada