Bio::DOOP::Cluster - DoOP cluster object
Version 0.10
This object represents a cluster. You can access properties through the methods. Usage: $cluster = Bio::DOOP::Cluster->new($db,"81007400","500"); print $cluster->get_cluster_id;
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
$cluster = Bio::DOOP::Cluster->new($db,"8010110","500"); Create a new cluster object from the cluster id and promoter type. Every promoter cluster has a uniq identifier. This is the cluster id. There are three promoter sizes (500,1000,3000 bp), so the uniq cluster is identified by two parameters : cluster id and promoter type. Return type: Bio::DOOP::Cluster object
Bio::DOOP::Cluster->new_by_id($db,"2453"); Used by internal MySQL queries. Return type: Bio::DOOP::Cluster object
$cluster_id = $cluster->get_id; Returns the MySQL id. Return type: string
Returns the cluster id. Return type: string
$pt = $cluster->get_promo_type; Returns the size of the promoter (500,1000,3000 bp). Return type: string
print $cluster->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
$date = $cluster->get_date; Returns the date when the cluster was last modified. Return type: string
print $cluster->get_version; Returns the version of the cluster. Return type: string
@subsets = @{$cluster->get_all_subsets}; Returns the arrayref of all subsets associated with the cluster. Return type: arrayref, the array containing Bio::DOOP::ClusterSubset objects
$subset = $cluster->get_subset_by_type("B"); if ($subset == -1){ print"No subset! Try another type\n"; } Returns the subset specified by type. Return type: Bio::DOOP::ClusterSubset object
@types = @{$cluster->get_available_types}; Returns all available cluster subset types. Return type: arrayref of string.
@seqs = @{$cluster->get_all_seqs}; Returns the arrayref of all sequences associated with the cluster. Return type: arrayref, the array containig Bio::DOOP::Sequence objects
@subsets = @{$cluster->get_orig_subset}; Returns the original subset, containing the whole cluster. Return type: Bio::DOOP::ClusterSubset object
$refseq = $cluster->get_ref_seq; Returns the cluster reference sequence (human or arabidopsis). Return type: Bio::DOOP::Sequence object
To install Bio::DOOP::DOOP, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DOOP::DOOP
CPAN shell
perl -MCPAN -e shell install Bio::DOOP::DOOP
For more information on module installation, please visit the detailed CPAN module installation guide.