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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bioperl-l@bio.perl.org
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:
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Email lstein@cshl.edu, simonf@cshl.edu
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
-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.
-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.
THIS METHOD CURRENTLY RETURNS EMPTY BECAUSE I CAN'T GET FETCH_BY_QUERY() TO WORK.
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
To install Bio::DB::Das::BioSQL, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DB::Das::BioSQL
CPAN shell
perl -MCPAN -e shell install Bio::DB::Das::BioSQL
For more information on module installation, please visit the detailed CPAN module installation guide.