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Bio::DB::UpdateableSeqUser Contributed Perl DocumentBio::DB::UpdateableSeqI(3)

NAME
       Bio::DB::UpdateableSeqI - An interface for writing to a database	of
       sequences.

SYNOPSIS
	   # get a Bio::DB::UpdateableSeqI somehow
	   eval	{
	       my ( @updatedseqs, @newseqs, @deadseqs);
	       my $seq = $db->get_Seq_by_id('ROA1_HUMAN');
	       $seq->desc('a new description');

	       push @updatedseqs, $seq;

	       $db->write_seq(\@updatedseqs, \@newseqs,	\@deadseqs);
	   };
	   if( $@ ) {
	       print STDERR "an	error when trying to write seq : $@\n";
	   }

DESCRIPTION
       This module seeks to provide a simple method for	pushing	sequence
       changes back to a Sequence Database - which can be an SQL compliant
       database, a file	based database,	AceDB, etc.

AUTHOR
       Jason Stajich <jason@bioperl.org>

   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

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   write_seq
	 Title	 : write_seq
	 Usage	 : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs)
	 Function: updates sequences in	first array,
		   adds	sequences in the second	array,
		   and removes sequences in the	third array.
	 Example :
	 Returns :
	 Args	 : arrays of sequence objects that must	be obtained from
		   Bio::DB::UpdateableSeqI.

   _add_seq
	Title	: _add_seq
	Usage	: _add_seq($seq)
	Function: Adds a new sequence
	Example	:
	Returns	: will throw an	exception if
		  sequences accession number already exists
	Args	: a new	seq object - should have an accession number

   _remove_seq
	Title	: _remove_seq
	Usage	: _remove_seq($seq)
	Function: Removes an existing sequence
	Example	:
	Returns	: will throw an	exception if
		  sequence does	not exists for the primary_id
	Args	: a seq	object that was	retrieved from Bio::DB::UpdateableSeqI

   _update_seq
	Title	: _update_seq
	Usage	: _update_seq($seq)
	Function: Updates a sequence
	Example	:
	Returns	: will throw an	exception if
		  sequence is out of sync from expected	val.
	Args	: a seq	object that was	retrieved from Bio::DB::UpdateableSeqI

Methods	inherieted from	Bio::DB::RandomAccessI
   get_Seq_by_id
	Title	: get_Seq_by_id
	Usage	: $seq = $db->get_Seq_by_id('ROA1_HUMAN')
	Function: Gets a Bio::Seq object by its	name
	Returns	: a Bio::Seq object
	Args	: the id (as a string) of a sequence
	Throws	: "id does not exist" exception

   get_Seq_by_acc
	Title	: get_Seq_by_acc
	Usage	: $seq = $db->get_Seq_by_acc('X77802');
	Function: Gets a Bio::Seq object by accession number
	Returns	: A Bio::Seq object
	Args	: accession number (as a string)
	Throws	: "acc does not	exist" exception

Methods	inheirited from	Bio::DB::SeqI
   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_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	: accession number (as a string)
	Throws	: "acc does not	exist" exception

perl v5.32.1			  2019-12-07	    Bio::DB::UpdateableSeqI(3)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR | APPENDIX | Methods inherieted from Bio::DB::RandomAccessI | Methods inheirited from Bio::DB::SeqI

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