Provided by: libbio-perl-perl_1.7.2-3_all
Bio::Index::AbstractSeq - base class for AbstractSeq
# Make a new sequence file indexing package package MyShinyNewIndexer; use base qw(Bio::Index::AbstractSeq); # Now provide the necessary methods...
Provides a common base class for multiple sequence files built using the Bio::Index::Abstract system, and provides a Bio::DB::SeqI interface.
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AUTHOR - Ewan Birney
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Bio::Index::Abstract, which provides dbm indexing for flat files of any type, containing sequence or not. Bio::Index::AbstractSeq inherits from Bio::Index::Abstract _file_format Title : _file_format Usage : $self->_file_format Function: Derived classes should override this method (it throws an exception here) to give the file format of the files used Example : Returns : Args : fetch Title : fetch Usage : $index->fetch( $id ) Function: Returns a Bio::Seq object from the index Example : $seq = $index->fetch( 'dJ67B12' ) Returns : Bio::Seq object Args : ID _get_SeqIO_object Title : _get_SeqIO_object Usage : $index->_get_SeqIO_object( $file ) Function: Returns a Bio::SeqIO object for the file Example : $seq = $index->_get_SeqIO_object( 0 ) Returns : Bio::SeqIO object Args : File number (an integer) get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id() Function: retrieves a sequence object, identically to ->fetch, but here behaving as a Bio::DB::BioSeqI Returns : new Bio::Seq object Args : string represents the id get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc() Function: retrieves a sequence object, identically to ->fetch, but here behaving as a Bio::DB::BioSeqI Returns : new Bio::Seq object Args : string represents the accession number get_PrimarySeq_stream Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::DB::SeqStreamI compliant object which provides a single method, next_primary_seq Returns : Bio::DB::SeqStreamI Args : none get_all_primary_ids Title : get_all_primary_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Example : Returns : an array of strings Args : none get_Seq_by_primary_id Title : get_Seq_by_primary_id Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string); Function: Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : primary id (as a string) Throws : "acc does not exist" exception