| Bio::Index::AbstractSeq(3pm) | User Contributed Perl Documentation | Bio::Index::AbstractSeq(3pm) |
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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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
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 :
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
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)
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
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
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
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
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
| 2021-08-15 | perl v5.32.1 |