Bio::DB::Das::BioSQL - DAS-style access to a BioSQL database


 # Open up a feature database
 $db = Bio::DB::Das::BioSQL->new(
                                 driver   => 'mysql',
                                 dbname => 'biosql',
                                 biodbname => 'test',
                                 host   => 'swiss',
                                 user   => 'lstein',
                                 pass   => undef,
                                 port   => undef,
                                 namespace   => 'namespace',
                                 version   => version_number,
                                ) or die;

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

  # segments are Bio::Das::SegmentI - compliant objects

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

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

  $error = $db->error;


Bio::DB::Das::BioSQL 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::DB::Das::Segment), 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::Das::FeatureTypeI (see Bio::Das::FeatureTypeI). Bio::DB::Das::BioSQL provides methods for interrogating the database for the types it contains and the counts of each type.


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AUTHORS - Lincoln Stein, Vsevolod (Simon) Ilyushchenko



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


 Title   : new
 Usage   : $db    = Bio::DB::Das::BioSQL(
                                    driver    => 'mysql',
                                    dbname    => 'biosql',
                                    biodbname => 'swissprot',
                                    host      => 'localhost',
                                    user      => 'jimbo',
                                    pass      => 'supersecret',
                                    port      => 3306,

 Function: Open up a Bio::DB::DasI interface to a BioSQL database
 Returns : a new Bio::DB::Das::BioSQL object
 Args    : See L<Bio::DB::Das::BioSQL::BioDatabaseAdaptor->new_from_registry()
           The new() method takes the same arguments exactly.


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

This method generates a Bio::Das::SegmentI object (see Bio::Das::SegmentI). 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::Das::SegmentI 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::Das::FeatureTypeI objects or a set of strings
             that can be converted into FeatureTypeI 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.

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


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

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

NOTE: This currently raises a "not-implemented" exception, as the BioSQL API does not appear to provide this functionality.


 Title   : search_notes
 Usage   : $db->search_notes($search_term,$max_results)
 Function: full-text search on features, ENSEMBL-style
 Returns : an array of [$name,$description,$score]
 Args    : see below
 Status  : public

This routine performs a full-text search on feature attributes (which attributes depend on implementation) and returns a list of [$name,$description,$score], where $name is the feature ID, $description is a human-readable description such as a locus line, and $score is the match strength.



 Title   : biosql
 Usage   : $biosql  = $db->biosql([$biosql])
 Function: Get/set the underlying Bio::DB::Das::BioSQL::BioDatabaseAdaptor
 Returns : An Bio::DB::Das::BioSQL::BioDatabaseAdaptor
 Args    : A new Bio::DB::Das::BioSQL::BioDatabaseAdaptor (optional)


 Title   : _segclass
 Usage   : $class = $db->_segclass
 Function: returns the perl class that we use for segment() calls
 Returns : a string containing the segment class
 Args    : none
 Status  : reserved for subclass use


 Title   : _adaptorclass
 Usage   : $class = $db->_adaptorclass
 Function: returns the perl class that we use as a BioSQL database adaptor
 Returns : a string containing the segment class
 Args    : none
 Status  : reserved for subclass use