NAME

Bio::DB::RandomAccessI - Abstract interface for a sequence database

SYNOPSIS

  #
  # get a database object somehow using a concrete class
  #

  $seq = $db->get_Seq_by_id('ROA1_HUMAN');

  #
  # $seq is a Bio::Seq object
  #

DESCRIPTION

This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement.

The Bio::DB::RandomAccessI class defines what methods a generic database class should have. At the moment it is just the ability to make Bio::Seq objects from a name (id) or an accession number.

CONTACT

Ewan Birney <birney@ebi.ac.uk> originally wrote this class.

Support

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.

Reporting Bugs

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://github.com/bioperl/bioperl-live/issues

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_Seq_by_id

 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
 Function: Gets a Bio::Seq object by its name
 Returns : a Bio::Seq object or undef if not found
 Args    : the id (as a string) of a sequence,

get_Seq_by_acc

 Title   : get_Seq_by_acc
 Usage   : $seq = $db->get_Seq_by_acc('X77802');
           $seq = $db->get_Seq_by_acc(Locus => 'X77802');
 Function: Gets a Bio::Seq object by accession number
 Returns : A Bio::Seq object or undef if not found
 Args    : accession number (as a string), or a two
               element list consisting of namespace=>accession
 Throws  : "more than one sequences correspond to this accession"
            if the accession maps to multiple primary ids and
            method is called in a scalar context

NOTE: The two-element form allows you to choose the namespace for the accession number.

get_Seq_by_version

 Title   : get_Seq_by_version
 Usage   : $seq = $db->get_Seq_by_version('X77802.1');
 Function: Gets a Bio::Seq object by sequence version
 Returns : A Bio::Seq object
 Args    : accession.version (as a string)
 Throws  : "acc.version does not exist" exception