Author image Endre Sebestyen
and 1 contributors

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;