Ewan Birney

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@chg.mc.duke.edu>

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 email or the web:

    bioperl-bugs@bioperl.org                   
    http://www.bioperl.org/bioperl-bugs/           

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