[Bioperl-l] registry configuration and access

[Michael Bradley]

If anyone can help me figure out why I can't access my locally indexed
files with the registry system I would greatly appreciate it. 
I have indexed some swissprot entries using bioflat_index.pl. This
appeared to work fine (no errors).
 
The config.dat file looks like this:
 
index   BerkeleyDB/1
format  URN:LSID:open-bio.org:swiss/protein
fileid_0        /home/bradley/PIPELINE/swissprot/uniprot_sprot.dat
575198688
primary_namespace       ID
secondary_namespaces    ACC     VERSION
 
The seqdatabase.ini file looks like this: 
 
[swissprot]
protocol=flat 
location=/home/bradley/biodb_index/registryspandtrembl
dbname=registrySPandTrEMBL
 
 
My problem starts when attempting to use the registry.
 
use Bio::DB::Registry;
my $registry = new Bio::DB::Registry;
my $sp = $registry->get_database('swissprot');
 
I am getting the following error: 
 
-------------------- 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/5.8.0/Bio/DB/Flat.pm:163
STACK Bio::DB::Flat::new_from_registry
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Flat.pm:254
STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Registry.pm:182
STACK Bio::DB::Registry::_load_registry
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Registry.pm:181
STACK Bio::DB::Registry::new
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Registry.pm:97
STACK toplevel
/home/bradley/PIPELINE/perl/scripts/Local_SP_EMBL_Retrieval.pl:232
 
--------------------------------------
 
By poking around in Flat.pm it appears that Flat.pm is unable to read
the index scheme from config.dat because it can't open config.dat.  I
know this because I edited the Flat.pm with two print statements and
only the first statement is executed :  
 
# read the configuration file
sub _read_config {
  my $self   = shift;
  my $path = $self->_config_path;
 
print "in sub _read_config\n";  ## this works  
 
  return unless -e $path;
 
print "reading config\n";  ## this doesn't execute
 
  open (F,$path) or $self->throw("open error on $path: $!");
  my %config;
  while (<F>) {
 
 
*****************************
Michael E. Bradley, Ph.D.
Postdoctoral Researcher
University of Florida
Department of Chemistry
Foundation for Applied 
Molecular Evolution
Ph. (352) 271-7005
Fax (353) 271-7076
 <mailto:mebradley at chem.ufl.edu> mebradley at chem.ufl.edu
****************************