DAS::GUS - DAS-style accession to a gus database
# Open up a feature database $db = DAS::GUS->new( -dsn => 'dbi:Oracle:sid=GUSDEV;host=localhost;port=1521', -user => 'user', -pass => 'pass', ); @segments = $db->segment ( -name => 'AAEE01000001', -start => 1, -end => 1000000 ); # segments are Bio::Das::SegmentI - compliant objects # fetch a list of features @features = $db->features( -type=>['type1', 'type2', 'type3'] ); # invoke a callback over features $db->features( -type=>['type1', 'type2', 'type3'], -callback => sub { ... } ); # get all featur 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;
Name: Haiming Wang Email: hwang@uga.edu
Title : new Usage : $db = DAS::GUS->new ( -dsn => 'dbi:Oracle:sid=GUSDEV;host=localhost;port=1521', -user => 'user', -pass => 'pass', ); Function : Open up a Bio::DB::DasI interface to a GUS database Returns : a new DAS::GUS object
Title : dbh Usage : $obj->dbh($newval) Function : get a database handle Returns : value of dbh (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : parser Usage : $obj->parser($parserObj) Function : get a sql parser object Returns : a sql parser object Args :
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::SegmentII). 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 version, 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. -atts Attribute of reference sequence
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 : fetures Usage : $db->features(@args) Function : get all features, possibly filtered by type Returns : a list of DAS::GUS::Segment::Feature 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 method and source.
-type List of feature types to return. Argument is an array of i reference containing strings of the format "method:source" -callback A callback to invoke on each feature. The subroutine will be passed each Bio::SeqFeatureI object in turn. -attributes A has reference containing attributes to match. -iterator Whether to return an iterator across the features
Types are indicated using the nomenclature "method:source". Either of these fields can be omitted, in which case a wildcard is used for the missing field. Type names without the colon (e.g. "exon") are interpreted as the method name and a source wild card. Regular expression are allowed in either field, as in: "similarity:BLAST.*".
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 match, 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 : get_feature_by_name Usage : $db->get_feature_by_name($class => $name) Function: fetch features by their name Returns : a list of DAS::GUS::Segment::Feature objects Args : the class and the name of the desired feature Status : public Note : You need to modify _feature_get() in Browser.pm currently. Find "return unless @segments;" and change it to "return @segments;" Debug it later. Also see multiple_choice() in gbrowse cgi script for getting features\'s attributes
To install CGI::Toggle, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CGI::Toggle
CPAN shell
perl -MCPAN -e shell install CGI::Toggle
For more information on module installation, please visit the detailed CPAN module installation guide.