Bio::DOOP::ClusterSubset - One subset of a cluster
Version 0.09
@cluster_subsets = @{$cluster->get_all_subsets};
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).
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
$cluster_subset = Bio::DOOP::ClusterSubset->new($db,"123"); You can create the object with the new method. The arguments are the following : Bio::DOOP::DBSQL object, subset_primary_id
print $cluster_subset->get_id; Prints out the subset primary id. This is the internal ID from the MySQL database. Return type: string.
print $cluster_subset->get_type; Prints out the subset type. Return type: string.
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
if ($cluster_subset->get_featno > 4){ print "We have lots of features!!!\n"; } get_featno returns the total number of features in the subset. Return type: string
get_motifno returns the number of motifs in the subset. Return type: string
if ($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')
$cluster_id = $cluster_subset->get_cluster; Returns the ID of the cluster, from which the subset originates. Return type: string
print $cluster_subset->get_dialign; Prints out the dialign format alignment of the subset. Return type: string
print $cluster_subset->get_fasta_align; Prints out the fasta format alignment of the subset. Return type: string
@motifs = @{$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
@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
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.