[Bioperl-l] registry configuration and access

Brian Osborne brian_osborne at cognia.com
Fri Jul 30 12:05:55 EDT 2004


Your seqdatabase.ini file is saying that there should be a directory called
/home/bradley/biodb_index/registryspandtrembl/registrySPandTrEMBL. Does this
directory exist?

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 Michael Bradley
Sent: Thursday, July 29, 2004 11:07 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] registry configuration and access

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
primary_namespace       ID
secondary_namespaces    ACC     VERSION

The seqdatabase.ini file looks like this:


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
STACK Bio::DB::Flat::new_from_registry
STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Registry.pm:182
STACK Bio::DB::Registry::_load_registry
STACK Bio::DB::Registry::new
STACK toplevel


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

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