[Bioperl-l] Bio::DB::Registry

[Brian Osborne]

Daniel,

I've made a change that fixes the OBDA/Registry system for me, but only when
I create "flat" indices with bioflat_index.pl, not "bdb". Now I'll take a
look at why "bdb" doesn't work, it has to do with the code's inability to
direct the search properly to BinarySearch.pm or BDB.pm, I think.
Anotherwords, using Bio::DB::Flat directly using "flat" (or "binarysearch")
or "bdb" works, but when you use Registry with "bdb" the search is
incorrectly directed to BinarySearch.

If you'd like to try this then get the latest Bioperl from CVS. I don't
think there's anything wrong with your config.dat, and no, I didn't make any
changes to bioflat_index.pl.


Brian O.

-----Original Message-----
From: Daniel Lang [mailto:daniel.lang at biologie.uni-freiburg.de]
Sent: Friday, October 17, 2003 3:29 PM
To: Brian Osborne
Subject: Re: [Bioperl-l] Bio::DB::Registry

Hi Brian,
No, I´ve tried it with the enviroment variable using both
methods(flat and bsd), but the error remains:(
I´v posted my config.dat to the list(Wed Oct 15 10:52:39
EDT 2003 ), maybe there is something wrong?
As I´ve mentioned, I´ve downladed the bioflat_index.pl
seperately from the attic...
I see you moved it back to examples, did you change
anything?

Thanks for your help!
Enjoy your weekend:)
Daniel