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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:

   http://bugzilla.open-bio.org/
 
 

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