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Bio::Index::AbstractSeUser Contributed Perl DocumentBio::Index::AbstractSeq(3)

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

perl v5.32.0			  2019-12-07	    Bio::Index::AbstractSeq(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney | APPENDIX | SEE ALSO

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