NAME
Bio::DOOP::Cluster - DoOP cluster object
VERSION
Version 0.12
SYNOPSIS
$cluster = Bio::DOOP::Cluster->new($db,"81007400","500");
print $cluster->get_cluster_id;DESCRIPTION
This object represents a cluster. You can access its properties through the methods.
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
new
Creates a new cluster object from the cluster id and promoter type. Every promoter cluster has a unique identifier. This is the cluster id. There are three promoter sizes (500,1000,3000 bp), so a unique cluster is identified by two parameters : cluster id and promoter type.
Return type: Bio::DOOP::Cluster object
$cluster = Bio::DOOP::Cluster->new($db,"8010110","500");new_by_id
Used by internal MySQL queries.
Return type: Bio::DOOP::Cluster object
Bio::DOOP::Cluster->new_by_id($db,"2453");get_id
Returns the MySQL id of the cluster
Return type: string
$cluster_id = $cluster->get_id;get_cluster_id
Returns the cluster id of the cluster.
Return type: string
$cluster_id = $cluster->get_cluster_id;get_promo_type
Returns the size of the promoter (500,1000,3000 bp).
Return type: string
$pt = $cluster->get_promo_type;get_type
Returns the type of the promoter (The available return types are the following: 1,2,3,4,5n,6n). See http://doop.abc.hu for more details.
Return type: string
print $cluster->get_type;get_date
Returns the date when the cluster was last modified.
Return type: string
$date = $cluster->get_date;get_version
Returns the version of the cluster.
Return type: string
print $cluster->get_version;get_all_subsets
Returns the arrayref of all subsets associated with the cluster.
Return type: arrayref, the array containing Bio::DOOP::ClusterSubset objects
@subsets = @{$cluster->get_all_subsets};get_subset_by_type
Returns a subset of a cluster, specified by type.
Return type: Bio::DOOP::ClusterSubset object
$subset = $cluster->get_subset_by_type("B");
if ($subset == -1){
print"No subsets! Try another subset type\n";
}get_available_types
Returns all available cluster subset types.
Return type: arrayref of strings
@types = @{$cluster->get_available_types};get_all_seqs
Returns the arrayref of all sequences associated with the cluster.
Return type: arrayref, the array containig Bio::DOOP::Sequence objects
@seqs = @{$cluster->get_all_seqs};get_orig_subset
Returns the original subset, containing the whole cluster.
Return type: Bio::DOOP::ClusterSubset object
@subsets = @{$cluster->get_orig_subset};get_ref_seq
Returns the cluster reference sequence (human or arabidopsis).
Return type: Bio::DOOP::Sequence object
$refseq = $cluster->get_ref_seq;