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

[Brian Osborne]

Daniel,

* MSG: you must specify an indexing scheme

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
you'll have to install if it's not installed. Check out the file
doc/howto/FLAT-DATABASES-HOWTO.txt.

We probably should convert this to Docbook, make it more accessible. Did you
take a look at the OBDA_Access HOWTO
(http://bioperl.org/HOWTOs/html/OBDA_Access.html)?

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 9:16 AM
To: Bioperl-List
Subject: [Bioperl-l] Bio::DB::Registry

Hi,
I encountered problems using the obda registry system...
Sequence retrieval with the example script fails:
        use Bio::DB::Registry();
        my $reg = new Bio::DB::Registry();
        my $db = $reg->get_database("ppp");
        my $seq = $db->get_Seq_by_acc("PPP_3085_C1");
        print $seq->seq,"\n";
With following Exception:
        -------------------- WARNING ---------------------
        MSG: Couldn't call new_from_registry on [Bio::DB::Flat]

        ------------- EXCEPTION  -------------
        MSG: you must specify an indexing scheme
        STACK Bio::DB::Flat::new
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Flat.pm:163
        STACK Bio::DB::Flat::new_from_registry
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Flat.pm:250
        STACK (eval) /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:194
        STACK Bio::DB::Registry::_load_registry
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:193
        STACK Bio::DB::Registry::new
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:96
        STACK toplevel fetch_test.pl:8

        --------------------------------------

        ---------------------------------------------------
        Can't call method "seq" on an undefined value at fetch_test.pl line
11,
<F> line 14.

I´m using latest tarball with Linux/Perl 5.61.
I indexed a flat fasta file using the bioflat_index.pl from the recent
tarball  with BDB. No Errors and warning.
I also created a /etc/bioinformatics/seqdatabase.ini as follows:
        VERSION=1.00

        [ppp]
        protocol=flat
        location=/export/flatfiles/ppp/
        dbname=ppp
The permissions for the corresponding directories should be ok also..
Any hints for me?

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

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