[Bioperl-l] bioperl-db bugs

[Jason Eric Stajich]

Markerdb is very much in flux because of the new schema Lincoln, Heikki,
and I have worked on.  The old objects are not being updated because we
are trying to decide how to build the mapping to bioperl objects -
bioperl-db will just be the bridge between the db schema and bioperl.  If
someone else is interested in marker and map dbs feel free to speak up, I
haven't had enough time to really clean things out.

All of these changes have no effect on the Sequence database (Seqdb)
modules - we just decided to cram everything related to a relationaldb in
one cvs module.  There is a stable tagged version of the working markerdb
but I don't know that it would be useful to anyone esp if we plan to
migrate to the new schema that is in the repository.  So options are to
continue to leave the HEAD broken and comment out the tests or try and
micro-fix things that are probably going to change soon.

-jason

On Fri, 19 Oct 2001, Elia Stupka wrote:

> Hello there,
>
> I am trying to fix the bugs that Alex reported.
> There is quite a few:
>
> 1)There is a strange one, Jason tell me if you seewhat you were trying to
> do here:
>
> In Bio/DB/Map/SQL/MarkerAdaptor.pm you write:
>
> my (undef,$chrom) = ( $marker->chrom =~ /(chr)?(X|Y|UL|\d+)/ );
>
> which perl doesn't like. I changed it to:
>
> my ($go,$chrom) = ( $marker->chrom =~ /(chr)?(X|Y|UL|\d+)/ );
>
> 2)Also, the marker-db.sql file had lots of commas on the last lines of the
> create statements, which made mysql die, I have fixed that.
>
> 3)The sql statements in the Adaptor were failing because statements were
> made on columns named mapid rather than map_id, name rather than map_name
> as in the sql file
>
> 4)The marker schema seems to have changed radically , but not the
> MarkerAdaptor.
>
> I am making fixes as we speak, but Jason maybe there is stuff you have not
> committed?
>
> Elia
>
>
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu