Christopher Fields > BioPerl-1.6.901 > Bio::DB::SeqI



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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924


Bio::DB::SeqI - Abstract Interface for Sequence databases


   # get a Bio::DB::SeqI somehow

   $seq = $seqdb->get_Seq_by_id('some-id');
   $seq = $seqdb->get_Seq_by_acc('some-accession-number');

   @ids = $seqdb->get_all_ids();
   $stream = $seqdb->get_PrimarySeq_stream();
   while((my $seq = $stream->next_seq()) {
      # $seq is a PrimarySeqI compliant object


Abstract interface for a sequence database


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AUTHOR - Ewan Birney ^



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

Methods inherieted from Bio::DB::RandomAccessI ^


 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


 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 [that were] specific for Bio::DB::SeqI ^


 Title   : get_PrimarySeq_stream
 Usage   : $stream = get_PrimarySeq_stream
 Function: Makes a Bio::SeqIO compliant object
           which provides a single method, next_seq
 Returns : Bio::SeqIO
 Args    : none


 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
 Example :
 Returns : an array of strings
 Args    : none


 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
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