NAME
Bio::DB::Das::BioSQL - DAS-style access to a BioSQL database
SYNOPSIS
# 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 );
# segments are Bio::Das::SegmentI - compliant objects
@segments = $db->segment(-name => 'NT_29921.4',
-start => 1,
-end => 1000000);
# fetch a list of features
@features = $db->features(-segment=>$segment, -type=>['type1','type2','type3']);
$stream = $db->get_seq_stream(-type=>['type1','type2','type3']);
# each feature is a Bio::SeqFeatureI-compliant object
while (my $feature = $stream->next_seq) {
# do something ...
}
# 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;DESCRIPTION
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 forinterrogating the database for the types it contains and the counts of each type.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bio.perl.orgReporting 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 email or the web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/AUTHORS
Lincoln Stein, Vsevolod (Simon) Ilyushchenko, Brian Osborne
Email lstein@cshl.edu, simonf@cshl.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
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.segment
Title : segment
Usage : $db->segment(@args);
Function: create a segment object
Returns : segment object(s)
Args : see belowThis 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.
-absoluteThe 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".
features
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 : publicThis 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.
-segment A segmentThe -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.
types
Title : types
Usage : $db->types(@args)
Function: return list of feature types in database
Returns : a list of Bio::Das::FeatureTypeI objects
Args : see belowThis 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 featuresThe 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.
search_notes
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 belowThis 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.
biosql
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)Accessor methods to return module names
get_seq_stream
Title : get_seq_stream
Usage : my $seqio = $self->get_seq_stream(-type => $types, -seq_id => $id)
Function: Performs a query and returns an iterator over it
Returns : a stream returning Bio::DB::Das::BioSQL::Feature objects
Args : -type, -seq_id, -start, -end
Types should be passed as an array reference or one string.
Use it like this:
$stream = $db->get_seq_stream(-type => 'exon', -seq_id => 'NC_122444');
while (my $exon = $stream->next_seq) {
print $exon->name,"\n";
}