NAME
Bio::DOOP::Util::Search - useful subrutines for easy search
VERSION
Version 0.05
SYNOPSIS
use Bio::DOOP::DOOP;
$db = Bio::DOOP::DBSQL->connect("doopuser","dooppasswd","doop-plant","localhost");
@motifs = @{Bio::DOOP::Util::Search::get_all_motifs_by_type($db,"V")};
DESCRIPTION
Collection of utilities managing big queries. Most of
the subrutines return arrayrefs of motifs, sequences, clusters.
For example: You want all the motifs that can be found in al of the
subsets. Instead of you go through all the motif in the jungle of
SQL querys, you use the ... subrutine. Your code will be more
simple.
AUTHOR
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
SUBRUTINES
get_all_motifs_by_type
Return the arrayref of all motifs that type is specified in the argument.
get_all_original_subset
Return the arrayref of all original subset.
get_all_cluster_by_gene_id
Return the arrayref of all clusters defined by the gene id
get_all_cluster_by_keyword
Return all clusters that is contain the keyword in its description, tss annotation or sequence xref
get_all_cluster_by_type
Return the arrayref of clusters that xref contain this type and value
get_all_cluster_by_taxon_name
Return the arrayref of clusters that is contain this taxon name
get_all_cluster_by_taxon_id
Return the arrayref of clusters that is contain this taxon id
get_all_cluster_by_sequence_id
Returns the arrayref of clusters containing the given sequence id (fake GI)
get_all_cluster_by_atno
Returns the arrayref of clusters containing the given At Number
get_all_seq_by_motifid
Return the arrayref of sequences containing the given motif id