Bio::Index::AbstractSeq(3pm) User Contributed Perl Documentation Bio::Index::AbstractSeq(3pm)
NAME
Bio::Index::AbstractSeq - base class for AbstractSeq
SYNOPSIS
# Make a new sequence file indexing package
package MyShinyNewIndexer;
use base qw(Bio::Index::AbstractSeq);
# Now provide the necessary methods...
DESCRIPTION
Provides a common base class for multiple sequence files built using the Bio::Index::Abstract system, and provides a Bio::DB::SeqI
interface.
FEEDBACK
Mailing Lists
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
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
SEE ALSO
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
perl v5.14.2 2012-03-02 Bio::Index::AbstractSeq(3pm)