Author image Endre Sebestyen
and 1 contributors

NAME

Bio::DOOP::ClusterSubset - One subset of a cluster

VERSION

Version 0.13

SYNOPSIS

  @cluster_subsets = @{$cluster->get_all_subsets};

DESCRIPTION

This object represents one subset of a cluster. A subset is a set of homologous sequences, hopefully monophyletic, grouped by evolutionary distance from the reference species (Arabidopsis or human).

AUTHORS

Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

METHODS

new

Creates a new subset object from the subset primary id. You usually won't need this, as you will create the subsets from a Bio::DOOP::Cluster object, based on the subset type.

Return type: Bio::DOOP::ClusterSubset object

  $cluster_subset = Bio::DOOP::ClusterSubset->new($db,"123");

get_id

Prints out the subset primary id. This is the internal ID from the MySQL database.

Return type: string

  print $cluster_subset->get_id;

get_type

Prints out the subset type.

Return type: string

  print $cluster_subset->get_type;

get_seqno

Returns the number of sequences in the subset.

Return type: string

  for(i = 0; i < $cluster_subset->get_seqno; i++){
      print $seq[$i];
  }

get_featno

Returns the total number of features (motifs, TSSs and other) in the subset.

Return type: string

  if ($cluster_subset->get_featno > 4){
      print "We have lots of features!!!\n";
  }

get_motifno

Returns the number of motifs in the subset.

Return type: string

  $motifs = $cluster_subset->get_motifno;

get_orig

Returns 'y' if the subset is the same as the original cluster, 'n' if not.

Return type: string ('y' or 'n')

  if ($cluster_subset->get_orig eq "y") {
      print "This is the original cluster!\n";
  }
  elsif ($cluster_subset->get_orig eq "n"){
      print "This is some smaller subset!\n";
  }

get_cluster

Returns the ID of the cluster, from which the subset originates.

Return type: string

  $cluster_id = $cluster_subset->get_cluster;

get_dialign

Prints out the dialign format alignment of the subset.

Return type: string

  print $cluster_subset->get_dialign;

get_fasta_align

Prints out the fasta format alignment of the subset.

Return type: string

  print $cluster_subset->get_fasta_align;

get_all_motifs

Returns the arrayref of all motifs associated with the subset.

Return type: arrayref, the array containig Bio::DOOP::Motif objects

  @motifs = @{$cluster_subset->get_all_motifs};

get_all_seqs

Returns a sorted arrayref of all sequences associated with the subset.

Sorting the sequences by the following criteria: The first sequence is always the reference species (Arabidopsis/Human). All other sequences are sorted first by the taxon_class (B E M V in the plants and P R E H M N T F V C in the chordates ) and then by the alphabetical order.

Return type: arrayref, the array containig Bio::DOOP::Sequence objects

  @seq = @{$cluster_subset->get_all_seqs};