Bio::DB UpdateableSeqI
SummaryIncluded librariesPackage variablesDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
Package variables
No package variables defined.
Inherit
Bio::DB::SeqI
Synopsis
No synopsis!
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.
Methods
write_seqDescriptionCode
_add_seqDescriptionCode
_remove_seqDescriptionCode
_update_seqDescriptionCode
Methods description
write_seqcode    nextTop
  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_seqcodeprevnextTop
 Title   : _add_seq
Usage : _add_seq($seq)
Function: Adds a new sequence
Example :
Returns : will throw an exception if
sequences accession number already exists
Args : a new seq object - should have an accession number
_remove_seqcodeprevnextTop
 Title   : _remove_seq
Usage : _remove_seq($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_seqcodeprevnextTop
 Title   : _update_seq
Usage : _update_seq($seq)
Function: Updates a sequence
Example :
Returns : will throw an exception if
sequence is out of sync from expected val.
Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI
Methods code
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self) = @_;
    
    $self->throw("Abstract database call of write_seq. Your database has not implemented this method!");
}
_add_seqdescriptionprevnextTop
sub _add_seq {
    my ($self ) = @_;
    
    $self->throw("Abstract database call of _add_seq. Your database has not implemented this method!");
}
_remove_seqdescriptionprevnextTop
sub _remove_seq {
    my ($self) = @_;
    
    $self->throw("Abstract database call of _remove_seq. Your database has not implemented this method!");
}
_update_seqdescriptionprevnextTop
sub _update_seq {
    my ($self) = @_;
    
    $self->throw("Abstract database call of _update_seq. Your database has not implemented this method!");
}
General documentation
SYNOPSIS Top
    # 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"; }
AUTHORTop
Jason Stajich <jason@bioperl.org>
Support Top
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 BugsTop
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/
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Methods inherieted from Bio::DB::RandomAccessITop
get_Seq_by_idTop
 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_accTop
 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::SeqITop
get_PrimarySeq_streamTop
 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_idsTop
 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_idTop
 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