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};