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Summary

Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file

Package variables

Included modules

Inherit

Bio::DB::Flat::BDB

Synopsis

See Bio::DB::Flat.

Description

This module allows embl files to be stored in Berkeley DB flat files
using the Open-Bio standard BDB-indexed flat file scheme. You should
not be using this directly, but instead use it via Bio::DB::Flat.

Methods

Methods description

None available.

Methods code

sub default_primary_namespace {

  return "ID";

}

sub default_secondary_namespaces {

  return qw(ACC);

}

sub parse_one_record {

  my $self  = shift;
  my $fh    = shift;
  my $parser =
    $self->{embl_cached_parsers}{fileno($fh)} ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format);
  my $seq = $parser->next_seq;
  my $ids = $self->seq_to_ids($seq);
  return $ids;

}

sub seq_to_ids {

  my $self = shift;
  my $seq  = shift;

  my $display_id = $seq->display_id;
  my $accession  = $seq->accession_number;
  my %ids;
  $ids{ID}       = $display_id;
  $ids{ACC}      = $accession   if defined $accession;
  return\% ids;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org             - General discussion
  http://bioperl.org/MailList.shtml - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email - lstein@cshl.org

Bio::DB::Flat,