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Summary

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

Package variables

Inherit

Bio::DB::Flat::BDB

Synopsis

See Bio::DB::Flat.

Description

This module allows swissprot 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_file_format {

 "swiss"

}

sub default_primary_namespace {

  return "ID";

}

sub default_secondary_namespaces {

  return qw(ACC VERSION);

}

sub seq_to_ids {

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

  my $display_id = $seq->display_id;
  my $accession  = $seq->accession_number;
  my $version    = $seq->seq_version;
  my $gi         = $seq->primary_id;
  my %ids;
  $ids{ID}       = $display_id;
  $ids{ACC}      = $accession              if defined $accession;
  $ids{VERSION}  = "$accession.$version"   if defined $accession && defined $version;
  return\% ids;
}


1;

}

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/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

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

  https://redmine.open-bio.org/projects/bioperl/

Bio::DB::Flat,

Email - lstein@cshl.org