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Bio::DB::UpdateableSeqI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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