@@ -1,5 +1,7 @@ #!/usr/bin/ruby require '../lib/locus_tree.rb' -container = LocusTree::Container.new(5, 50) -container.bulk_load('first_mio.gff') +bin_size = 4000 +nr_children = 2 + +@container = LocusTree::Container.new(bin_size, nr_children, 'locus_tree_' + bin_size.to_s + '.sqlite3', 'genes.txt') \ No newline at end of file samples/create_index.rb @@ -1,9 +1,26 @@ #!/usr/bin/ruby require '../lib/locus_tree.rb' -container = LocusTree::Container.open('locus_tree.sqlite3') -results = container.search(Locus.new('1', 500, 700000), 1) +bin_size = 4000 +nr_children = 2 -results.each do |r| - puts r.locus.to_s + "\t" + r.value.to_s +@container = LocusTree::Container.load_structure('locus_tree_' + bin_size.to_s + '.sqlite3') + +positive_nodes = @container.query('2', 143570450, 143571890, bin_size.div(10)) +positive_nodes.each do |node| + puts node.to_s + "\t" + node.value.to_s +end + +positive_nodes = @container.query('2', 143570450, 143671890, bin_size + 1) +positive_nodes.each do |node| + puts node.to_s + "\t" + node.value.to_s end + +positive_nodes = @container.query('2', 143570450, 143671890, nr_children*bin_size + 1) +positive_nodes.each do |node| + puts node.to_s + "\t" + node.value.to_s +end + +puts @container.query_single_bin('24', 500, 50_000).to_s +puts @container.query_single_bin('24', 49_050, 49_500).to_s +puts @container.query_single_bin('24', 999_999, 1_000_002).to_s \ No newline at end of file samples/search_index.rb bf4768da9c17fa87bb3681bd69a3d0d173e5fd87 Jan Aerts jan.aerts@gmail.com http://github.com/jandot/locustree/commit/e93a144179d61c71a849067b476a6cffab72c9be e93a144179d61c71a849067b476a6cffab72c9be 2009-07-31T02:25:50-07:00 2009-07-31T02:25:50-07:00 Changed sample files bd42b0047077bf23f7c8a4ca05996a0ceeeca384 Jan Aerts jan.aerts@gmail.com