[BioPython] Re: [BioSQL-l] python

[Brad Chapman]

Hi Christen;
[Hilmar -- thanks for forwarding; I should sign up for BioSQL]

> >I have tried to get working biosql under mysql and python as ewplained 
> >in Basic BioSQL with Biopoython
> >I have donwloaded the latest version of both, and tried the example 
> >with cor6_6.gb
> >
> >then I got numerous problems
[...]
> >My questions are :
> >Is there somebody else having trouble, or do you I miss something ?

The short answer is that the Biopython implementation is not fully
up and compliant with the current BioSQL schema. Yves Bastide sent
in some patches back in September which were checked in:

http://www.biopython.org/pipermail/biopython-dev/2003-September/001485.html

So they should be in the latest version (1.23), if you are using
that. They were not well checked over by me (or anyone else that I'm
aware) but are definitely at least a starting point.

> >If I did it right, Is there somebody else trying to fix these
> >problems?

I don't know of anyone working on it right now. It is definitely of
interest to me to fix, but I haven't had the opportunity (and have
also been saying that for a while now). We definitely welcome some
help on this front.

If you just need to get something done quickly and aren't worried
about compatibility with the current schema, the (older) schemas in
biopython/Tests/BioSQL (biosqldb-mysql.sql and biosqldb-pg.sql)
should work with the current code.

> >If things need some help, it would be very nice to have some clear
> >description of biosql structure. I have not been able to find it. 
> >Somebody could help ?

Yves might be able to help as he has been looking at this most
recently. Hopefully he's around and be more specific than I can.

Hope this helps.
Brad