Bio::DOOP::Util::Search - Useful methods for easy search

Bio-DOOP-DOOP documentation Contained in the Bio-DOOP-DOOP distribution.

Index

Code Index:

NAME

Top

Bio::DOOP::Util::Search - Useful methods for easy search

VERSION

Top

Version 0.13

SYNOPSIS

Top

  use Bio::DOOP::DOOP;

  $db = Bio::DOOP::DBSQL->connect("user","passwd","database","localhost");
  @motifs = @{Bio::DOOP::Util::Search::get_all_motifs_by_type($db,"V")};

DESCRIPTION

Top

Collection of utilities handling large queries. Most of the methods return arrayrefs of motifs, sequences or clusters.

AUTHORS

Top

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

METHODS

Top

get_all_motifs_by_type

Returns the arrayref of motifs with the type specified in the arguments.

get_all_original_subset

Returns the arrayref of all original subsets.

get_all_cluster_by_gene_id

Returns the arrayref of all Bio::DOOP::Cluster objects, defined by a gene id.

get_all_cluster_by_keyword

Returns the arrayref of all Bio::DOOP::Cluster objects, containing the keyword in their description or tss annotation.

get_all_cluster_by_xref

Returns the arrayref of Bio::DOOP::Clsuter objects, containing a given xref.

get_all_cluster_by_taxon_name

Returns the arrayref of Bio::DOOP::Cluster objects containing a taxon name. Don't use this, use get_all_cluster_by_taxon_id with NCBI IDs!

get_all_cluster_id_by_taxon_name

Returns the arrayref of cluster ids containing the taxon name. Don't use this, use get_all_cluster_by_taxon_id with NCBI IDs!

get_all_cluster_by_taxon_id

Returns the arrayref of Bio::DOOP::Cluster objects, containing an NCBI taxon id.

get_all_cluster_id_by_taxon_id

Returns the arrayref of cluster ids containing an NCBI taxon id.

get_all_cluster_by_sequence_id

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given sequence id (fake GI).

get_all_cluster_by_atno

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given At Number.

get_all_seq_by_motifid

Returns the arrayref of Bio::DOOP::Sequence objects, containing a given motif id.

get_all_cluster_by_go_id

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given GO ID.

get_all_cluster_by_ensno

Returns the arrayref of Bio::DOOP::Cluster objects, containing a given ENSEMBL gene ID.

get_all_cluster_id

Returns an arrayref of all the cluster IDs of a given promoter/subset category. For example returns all clusters with 1000 bp E type subsets.

Bio-DOOP-DOOP documentation Contained in the Bio-DOOP-DOOP distribution. 
package Bio::DOOP::Util::Search;

use strict;
use warnings;


our $VERSION = '0.13';


sub get_all_motifs_by_type {
  my $db                   = shift;
  my $type                 = shift;

  my @motifs;
  my $ret = $db->query("SELECT motif_feature_primary_id FROM motif_feature WHERE motif_type = \"$type\";");
  for my $motif_id (@$ret){
	  push @motifs,Bio::DOOP::Motif->new($db,$$motif_id[0]);
  }
  return(\@motifs);
}


sub get_all_original_subset {
  my $db                   = shift;
  my @subsets;
  my $ret = $db->query("SELECT subset_primary_id FROM cluster_subset WHERE original = \"y\";");
  for my $subset (@$ret){
	  push @subsets,Bio::DOOP::ClusterSubset->new($db,$$subset[0]);
  }
  return(\@subsets);
}


sub get_all_cluster_by_gene_id  {
  my $db                   = shift;
  my $gene_id              = shift;
  my $promoter_size        = shift;

  my @clusters;
  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster,sequence,subset_xref,sequence_annotation WHERE sequence.sequence_annotation_primary_id = sequence_annotation.sequence_annotation_primary_id AND subset_xref.sequence_primary_id = sequence.sequence_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND sequence_annotation.sequence_gene_name LIKE '$gene_id%';");

  for my $cluster (@$ret){
          push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
  }
  return(\@clusters);
}


sub get_all_cluster_by_keyword {
  my $db                   = shift;
  my $keyword              = shift;
  my $promoter_size        = shift;

  my @clusters;
  my @cluster_db_id;
  my %seen;

  # Query from sequence_annot.
  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, sequence_annotation, sequence, subset_xref WHERE subset_xref.sequence_primary_id = sequence.sequence_primary_id AND sequence.sequence_annotation_primary_id = sequence_annotation.sequence_annotation_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND sequence_annotation.sequence_desc LIKE '%$keyword%';");
    for my $cluster (@$ret){
          push @cluster_db_id,$$cluster[0];
  }

  # Query from tss_annot.
  # NO
  #$ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, tss_annotation, sequence_feature, subset_xref WHERE subset_xref.sequence_primary_id = sequence_feature.sequence_primary_id AND sequence_feature.tss_primary_id = tss_annotation.tss_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND tss_annotation.tss_desc LIKE '%$keyword%';");
  #for my $cluster (@$ret){
  #        push @cluster_db_id,$$cluster[0];
  #}

  #Remove the redundant cluster_db_ids.
  my @cluster_id_uniq = grep { ! $seen{ $_ }++ } @cluster_db_id;

  for my $cluster (@cluster_id_uniq){
          push @clusters,Bio::DOOP::Cluster->new($db,$cluster,$promoter_size);
  }
  
  return(\@clusters);
}


sub get_all_cluster_by_xref {
  my $db                   = shift;
  my $type                 = shift;
  my $value                = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, sequence_xref, subset_xref WHERE sequence_xref.sequence_primary_id = subset_xref.sequence_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND sequence_xref.xref_type = '$type' AND sequence_xref.xref_id = '$value';");

  for my $cluster (@$ret){
	  push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
  }

  return(\@clusters);
}


sub get_all_cluster_by_taxon_name {
  my $db                   = shift;
  my $taxon                = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, taxon_annotation, sequence, subset_xref WHERE subset_xref.sequence_primary_id = sequence.sequence_primary_id AND sequence.taxon_primary_id = taxon_annotation.taxon_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND taxon_annotation.taxon_name = '$taxon';");

  for my $cluster (@$ret){
	  push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
  }
  return(\@clusters);
}


sub get_all_cluster_id_by_taxon_name {
  my $db                   = shift;
  my $taxon                = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, taxon_annotation, sequence, subset_xref WHERE subset_xref.sequence_primary_id = sequence.sequence_primary_id AND sequence.taxon_primary_id = taxon_annotation.taxon_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND taxon_annotation.taxon_name = '$taxon';");

  for my $cluster (@$ret){
	  push @clusters,$$cluster[0];
  }
  return(\@clusters);
}


sub get_all_cluster_by_taxon_id {
  my $db                   = shift;
  my $taxon                = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, taxon_annotation, sequence, subset_xref WHERE subset_xref.sequence_primary_id = sequence.sequence_primary_id AND sequence.taxon_primary_id = taxon_annotation.taxon_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND taxon_annotation.taxon_taxid = '$taxon';");

  for my $cluster (@$ret){
	  push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
  }
  return(\@clusters);
}


sub get_all_cluster_id_by_taxon_id {
  my $db                   = shift;
  my $taxon                = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, taxon_annotation, sequence, subset_xref WHERE subset_xref.sequence_primary_id = sequence.sequence_primary_id AND sequence.taxon_primary_id = taxon_annotation.taxon_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND taxon_annotation.taxon_taxid = '$taxon';");

  for my $cluster (@$ret){
	  push @clusters,$$cluster[0];
  }
  return(\@clusters);
}


sub get_all_cluster_by_sequence_id {
  my $db                   = shift;
  my $sequence_id          = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, sequence, subset_xref WHERE subset_xref.sequence_primary_id = sequence.sequence_primary_id AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND sequence.sequence_fake_gi LIKE '$sequence_id%';");

  for my $cluster (@$ret){
	push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
  }
  return(\@clusters);
}


sub get_all_cluster_by_atno {
  my $db                   = shift;
  my $atno                 = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, sequence_xref, subset_xref WHERE subset_xref.sequence_primary_id = sequence_xref.sequence_primary_id AND sequence_xref.xref_type = 'at_no' AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND sequence_xref.xref_id LIKE '$atno%';");

  for my $cluster (@$ret) {
	push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
  }
  return(\@clusters);
}


sub get_all_seq_by_motifid {
  my $db                   = shift;
  my $motifid              = shift;
  my @seqs;

  my $ret = $db->query("SELECT sequence_primary_id FROM sequence_feature WHERE motif_feature_primary_id = $motifid;");

  for my $seq (@$ret){
      push @seqs,Bio::DOOP::Sequence->new($db,$$seq[0]);
  }

  return(\@seqs);
}


sub get_all_cluster_by_go_id {
	my $db            = shift;
	my $goid          = shift;
	my $promoter_size = shift;

	my @clusters;

	my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, sequence_xref, subset_xref WHERE subset_xref.sequence_primary_id = sequence_xref.sequence_primary_id AND sequence_xref.xref_type = 'go_id' AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND sequence_xref.xref_id LIKE '$goid';");

	for my $cluster (@$ret) {
		push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
	}
	return(\@clusters);
}


sub get_all_cluster_by_ensno {
  my $db                   = shift;
  my $ensno                = shift;
  my $promoter_size        = shift;

  my @clusters;

  my $ret = $db->query("SELECT DISTINCT(cluster.cluster_id) FROM cluster, sequence_xref, subset_xref WHERE subset_xref.sequence_primary_id = sequence_xref.sequence_primary_id AND sequence_xref.xref_type = 'ensembl_id' AND cluster.cluster_primary_id = subset_xref.cluster_primary_id AND sequence_xref.xref_id LIKE '$ensno%';");

  for my $cluster (@$ret) {
	push @clusters,Bio::DOOP::Cluster->new($db,$$cluster[0],$promoter_size);
  }
  return(\@clusters);
}


sub get_all_cluster_id {

	my $db            = shift;
	my $promoter_size = shift;
	my $subset_type   = shift;

	my @clusters;

	my $ret = $db->query("SELECT cluster.cluster_id FROM cluster, cluster_subset WHERE cluster.cluster_promoter_type = '$promoter_size' AND cluster.cluster_primary_id = cluster_subset.cluster_primary_id AND cluster_subset.subset_type = '$subset_type';");

	for my $cluster (@$ret) {
		push @clusters, $$cluster[0];
	}
	return(\@clusters);
}
1;