Bio::DB::RandomAccessI - Abstract interface for a sequence database
# # get a database object somehow using a concrete class # $seq = $db->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object #
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 a accession number.
Ewan Birney originally wrote this class.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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,
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.
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