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

[Brian Osborne]

Daniel,

Hmm. Here's a config.dat that worked for me:

index   BerkeleyDB/1
format  URN:LSID:open-bio.org:fasta/protein
fileid_0        /home/bosborne/programming/perl/Bioperl/out.fa  7405
primary_namespace       ACC
secondary_namespaces

Note that I'm saying "fasta/protein", not simply "fasta". Don't know if it's
important.

I'll look into bioflat_index.pl.

Brian O.



-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Daniel Lang
Sent: Wednesday, October 15, 2003 10:53 AM
To: Brian Osborne; Bioperl-List
Subject: Re: [Bioperl-l] Bio::DB::Registry

Thanks Brian, but still not working:(

On Wednesday 15 October 2003 16:31, Brian Osborne wrote:
> My guess is that you need to set the variable OBDA_INDEX. A value of
"flat"
> means use the built-in scheme, a value of "bdb" means use BerkeleyDB,
which
I tried both flat and bdb with the corresponding  OBDA_INDEX enviroment
variable  setting.

> (http://bioperl.org/HOWTOs/html/OBDA_Access.html)?
Yes I configured everything correspondingly.

I was also confused, that in the current cvs the bioflat_index.pl script can
only be found in scripts/DB/attic and not in examples/db?
So the version I´m using is the one from attic...

Maybe somehing is wrong with my config.dat:
index   flat/1
fileid_0        /export/flatfiles/ppp.seq       13155893
primary_namespace       ACC
secondary_namespaces    ID
format  URN:LSID:open-bio.org:fasta

Thanks in advance,
Daniel


--
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

#################################################
>REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################


_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l