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

cpanm CGI::Toggle

perl -MCPAN -e shell
install CGI::Toggle