Ewan Birney


Bio::DasI - DAS-style access to a feature database


  # Open up a feature database somehow...

  @segments = $db->segment(-name  => 'NT_29921.4',
                           -start => 1,
                           -end   => 1000000);

  # segments are Bio::DasSegmentI - compliant objects

  # fetch a list of features
  @features = $db->features(-type=>['type1','type2','type3']);

  # invoke a callback over features
                -callback => sub { ... }

  $stream   = $db->get_seq_stream(-type=>['type1','type2','type3']);
  while (my $feature = $stream->next_seq) {
     # each feature is a Bio::SeqFeatureI-compliant object

  # get all feature types
  @types   = $db->types;

  # count types
  %types   = $db->types(-enumerate=>1);

  @feature = $db->get_feature_by_name($name);
  @feature = $db->get_feature_by_id($id);
  @feature = $db->get_feature_by_target($target_name);
  @feature = $db->get_feature_by_attribute($att1=>$value1,$att2=>$value2);

  $error = $db->error;


Bio::DasI is a simplified alternative interface to sequence annotation databases used by the distributed annotation system (see Bio::Das). In this scheme, the genome is represented as a series of features, a subset of which are named. Named features can be used as reference points for retrieving "segments" (see Bio::DasSegmentI), and these can, in turn, be used as the basis for exploring the genome further.

In addition to a name, each feature has a "class", which is essentially a namespace qualifier and a "type", which describes what type of feature it is. Das uses the GO consortium's ontology of feature types, and so the type is actually an object of class Bio::DasFeatureTypeI (see Bio::DasFeatureTypeI). Bio::DasI provides methods for interrogating the database for the types it contains and the counts of each type.


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AUTHOR - Lincoln Stein

Email lstein@cshl.org


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


 Title   : types
 Usage   : $db->types(@args)
 Function: return list of feature types in database
 Returns : a list of Bio::DasFeatureTypeI objects
 Args    : see below

This routine returns a list of feature types known to the database. It is also possible to find out how many times each feature occurs.

Arguments are -option=>value pairs as follows:

  -enumerate  if true, count the features

The returned value will be a list of Bio::DasFeatureTypeI objects (see Bio::DasFeatureTypeI.

If -enumerate is true, then the function returns a hash (not a hash reference) in which the keys are the stringified versions of Bio::DasFeatureTypeI and the values are the number of times each feature appears in the database.


 Title   : segment
 Usage   : $db->segment(@args);
 Function: create a segment object
 Returns : segment object(s)
 Args    : see below

This method generates a Bio::DasSegmentI object (see Bio::DasSegmentI). The segment can be used to find overlapping features and the raw sequence.

When making the segment() call, you specify the ID of a sequence landmark (e.g. an accession number, a clone or contig), and a positional range relative to the landmark. If no range is specified, then the entire region spanned by the landmark is used to generate the segment.

Arguments are -option=>value pairs as follows:

 -name         ID of the landmark sequence.

 -class        A namespace qualifier.  It is not necessary for the
               database to honor namespace qualifiers, but if it
               does, this is where the qualifier is indicated.

 -version      Version number of the landmark.  It is not necessary for
               the database to honor versions, but if it does, this is
               where the version is indicated.

 -start        Start of the segment relative to landmark.  Positions
               follow standard 1-based sequence rules.  If not specified,
               defaults to the beginning of the landmark.

 -end          End of the segment relative to the landmark.  If not specified,
               defaults to the end of the landmark.

The return value is a list of Bio::DasSegmentI objects. If the method is called in a scalar context and there are no more than one segments that satisfy the request, then it is allowed to return the segment. Otherwise, the method must throw a "multiple segment exception".


 Title   : features
 Usage   : $db->features(@args)
 Function: get all features, possibly filtered by type
 Returns : a list of Bio::SeqFeatureI objects
 Args    : see below
 Status  : public

This routine will retrieve features in the database regardless of position. It can be used to return all features, or a subset based on their type

Arguments are -option=>value pairs as follows:

  -types     List of feature types to return.  Argument is an array
             of Bio::DasFeatureTypeI objects.

  -callback   A callback to invoke on each feature.  The subroutine
              will be passed each Bio::SeqFeatureI object in turn.

  -attributes A hash reference containing attributes to match.

The -attributes argument is a hashref containing one or more attributes to match against:

  -attributes => { Gene => 'abc-1',
                   Note => 'confirmed' }

Attribute matching is simple exact string matching, and multiple attributes are ANDed together. See Bio::DB::ConstraintsI for a more sophisticated take on this.

If one provides a callback, it will be invoked on each feature in turn. If the callback returns a false false value, iteration will be interrupted. When a callback is provided, the method returns undef.


 Title   : get_seq_stream
 Usage   : my $seqio = $self->get_seq_sream(@args)
 Function: Performs a query and returns an iterator over it
 Returns : a Bio::SeqIO stream capable of returning Bio::DasSegmentI objects
 Args    : As in features()
 Status  : public

This routine takes the same arguments as features(), but returns a Bio::SeqIO::Stream-compliant object. Use it like this:

  $stream = $db->get_seq_stream('exon');
  while (my $exon = $stream->next_seq) {
     print $exon,"\n";

NOTE: In the interface this method is aliased to get_feature_stream(), as the name is more descriptive.