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

[Daniel Lang]

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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