NAME
Bio::DOOP::ClusterSubset - One subset of a cluster
VERSION
Version 0.09
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).
AUTHOR
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
new
$cluster_subset = Bio::DOOP::ClusterSubset->new($db,"123");
You can create the object with the new method.
The arguments are the following : Bio::DOOP::DBSQL object, subset_primary_id
get_id
print $cluster_subset->get_id;
Prints out the subset primary id. This is the internal ID from the MySQL database.
Return type: string.
get_type
print $cluster_subset->get_type;
Prints out the subset type.
Return type: string.
get_seqno
for(i = 0; i < $cluster_subset->get_seqno; i++){
print $seq[$i];
}
Prints out all sequences linked to the subset.
get_seqno returns the number of sequences in the
subset.
Return type: string
get_featno
if ($cluster_subset->get_featno > 4){
print "We have lots of features!!!\n";
}
get_featno returns the total number of features in the
subset.
Return type: string
get_motifno
get_motifno returns the number of motifs in the
subset.
Return type: string
get_orig
if ($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";
}
Return type: string ('y' or 'n')
get_cluster
$cluster_id = $cluster_subset->get_cluster;
Returns the ID of the cluster, from which the subset originates.
Return type: string
get_dialign
print $cluster_subset->get_dialign;
Prints out the dialign format alignment of the subset.
Return type: string
get_fasta_align
print $cluster_subset->get_fasta_align;
Prints out the fasta format alignment of the subset.
Return type: string
get_all_motifs
@motifs = @{$cluster_subset->get_all_motifs};
Returns the arrayref of all motifs associated with the subset.
Return type: arrayref, the array containig Bio::DOOP::Motif objects
get_all_seqs
@seq = @{$cluster_subset->get_all_seqs};
Returns the arrayref of all sequences associated with the subset.
Return type: arrayref, the array containig Bio::DOOP::Sequence objects