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://github.com/bioperl/bioperl-live/issues

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq