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/ DAS::GUS

NAME

DAS::GUS - DAS-style accession to a gus database

SYNOPSIS


            

              
              
# 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;

AUTHOR

Name: Haiming Wang Email: hwang@uga.edu

new


            

              
              
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

dbh


            

              
              
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)

parser


            

              
              
Title           : parser
Usage           : $obj->parser($parserObj)
Function  : get a sql parser object
Returns : a sql parser object
Args            :

segment


            

              
              
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".

features


            

              
              
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.

Arguments are -option=>value pairs as follows:


            

              
              
-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.

get_feature_by_name


            

              
              
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