finishm 0.0.1

data/spec/depth_first_search_spec.rb

@@ -0,0 +1,190 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "DepthFirstSearch" do
+  it 'should traverse a linear array' do
+    Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug');
+    Bio::Log::LoggerPlus.new 'bio-velvet'; Bio::Log::CLI.configure 'bio-velvet'
+
+    graph = Bio::Velvet::Graph.new
+    node1 = Bio::Velvet::Graph::Node.new
+    node1.node_id = 1
+    node2 = Bio::Velvet::Graph::Node.new
+    node2.node_id = 2
+    node3 = Bio::Velvet::Graph::Node.new
+    node3.node_id = 3
+    array = Bio::Velvet::Graph::NodeArray.new
+    array[1] = node1
+    array[2] = node2
+    array[3] = node3
+    arc1 = Bio::Velvet::Graph::Arc.new
+    arc1.begin_node_id = 1
+    arc1.end_node_id = 2
+    arc1.begin_node_direction = true
+    arc1.end_node_direction = true
+    arc2 = Bio::Velvet::Graph::Arc.new
+    arc2.begin_node_id = 2
+    arc2.end_node_id = 3
+    arc2.begin_node_direction = true
+    arc2.end_node_direction = true
+    arc_array = Bio::Velvet::Graph::ArcArray.new
+    arc_array.push arc1
+    arc_array.push arc2
+    graph.nodes = array
+    graph.arcs = arc_array
+
+
+    onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+    onode.node = node1
+    onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+
+    expecteds = [1,2,3]
+    founds = []
+
+    graph.depth_first_search(onode) do |onode|
+      founds.push onode.last.node.node_id
+    end
+    founds.should == expecteds
+  end
+
+  it 'should traverse a bubble' do
+    graph = Bio::Velvet::Graph.new
+    node1 = Bio::Velvet::Graph::Node.new
+    node1.node_id = 1
+    node2 = Bio::Velvet::Graph::Node.new
+    node2.node_id = 2
+    node3 = Bio::Velvet::Graph::Node.new
+    node3.node_id = 3
+    node4 = Bio::Velvet::Graph::Node.new
+    node4.node_id = 4
+    array = Bio::Velvet::Graph::NodeArray.new
+    array[1] = node1
+    array[2] = node2
+    array[3] = node3
+    array[4] = node4
+    graph.nodes = array
+
+    arc_array = Bio::Velvet::Graph::ArcArray.new
+    graph.arcs = arc_array
+    arc = Bio::Velvet::Graph::Arc.new
+    arc.begin_node_id = 1
+    arc.end_node_id = 2
+    arc.begin_node_direction = true
+    arc.end_node_direction = true
+    arc_array.push arc
+    arc = Bio::Velvet::Graph::Arc.new
+    arc.begin_node_id = 2
+    arc.end_node_id = 4
+    arc.begin_node_direction = true
+    arc.end_node_direction = true
+    arc_array.push arc
+    arc = Bio::Velvet::Graph::Arc.new
+    arc.begin_node_id = 1
+    arc.end_node_id = 3
+    arc.begin_node_direction = true
+    arc.end_node_direction = true
+    arc_array.push arc
+    arc = Bio::Velvet::Graph::Arc.new
+    arc.begin_node_id = 3
+    arc.end_node_id = 4
+    arc.begin_node_direction = true
+    arc.end_node_direction = true
+    arc_array.push arc
+
+    onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+    onode.node = node1
+    onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+
+    expecteds = [1,2,4,3]
+    founds = []
+
+    graph.depth_first_search(onode) do |onode|
+      founds.push onode.last.node.node_id
+    end
+    founds.should == expecteds
+  end
+
+  it 'should deal with cycles' do
+    graph = Bio::Velvet::Graph.new
+    node1 = Bio::Velvet::Graph::Node.new
+    node1.node_id = 1
+    node2 = Bio::Velvet::Graph::Node.new
+    node2.node_id = 2
+    array = Bio::Velvet::Graph::NodeArray.new
+    array[1] = node1
+    array[2] = node2
+    graph.nodes = array
+
+    arc_array = Bio::Velvet::Graph::ArcArray.new
+    graph.arcs = arc_array
+    arc = Bio::Velvet::Graph::Arc.new
+    arc.begin_node_id = 1
+    arc.end_node_id = 2
+    arc.begin_node_direction = true
+    arc.end_node_direction = true
+    arc_array.push arc
+    arc = Bio::Velvet::Graph::Arc.new
+    arc.begin_node_id = 2
+    arc.end_node_id = 2
+    arc.begin_node_direction = true
+    arc.end_node_direction = true
+    arc_array.push arc
+
+    onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+    onode.node = node1
+    onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+
+    expecteds = [1,2]
+    founds = []
+
+    graph.depth_first_search(onode) do |onode|
+      founds.push onode.last.node.node_id
+    end
+    founds.should == expecteds
+  end
+
+  it 'should stop when asked' do
+    Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug');
+    Bio::Log::LoggerPlus.new 'bio-velvet'; Bio::Log::CLI.configure 'bio-velvet'
+
+    graph = Bio::Velvet::Graph.new
+    node1 = Bio::Velvet::Graph::Node.new
+    node1.node_id = 1
+    node2 = Bio::Velvet::Graph::Node.new
+    node2.node_id = 2
+    node3 = Bio::Velvet::Graph::Node.new
+    node3.node_id = 3
+    array = Bio::Velvet::Graph::NodeArray.new
+    array[1] = node1
+    array[2] = node2
+    array[3] = node3
+    arc1 = Bio::Velvet::Graph::Arc.new
+    arc1.begin_node_id = 1
+    arc1.end_node_id = 2
+    arc1.begin_node_direction = true
+    arc1.end_node_direction = true
+    arc2 = Bio::Velvet::Graph::Arc.new
+    arc2.begin_node_id = 2
+    arc2.end_node_id = 3
+    arc2.begin_node_direction = true
+    arc2.end_node_direction = true
+    arc_array = Bio::Velvet::Graph::ArcArray.new
+    arc_array.push arc1
+    arc_array.push arc2
+    graph.nodes = array
+    graph.arcs = arc_array
+
+
+    onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+    onode.node = node1
+    onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+
+    expecteds = [1]
+    founds = []
+
+    graph.depth_first_search(onode) do |onode|
+      founds.push onode.last.node.node_id
+      false
+    end
+    founds.should == expecteds
+  end
+end

data/spec/dijkstra_spec.rb

@@ -0,0 +1,143 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Dijkstra" do
+  describe 'min distances' do
+
+    "SOME OF THIS IS LIKELY TESTED IN OTHER FILES SO GO LOOKING BEFORE NEW TESTS ARE WRITTEN"
+
+    it 'should do hello world' do
+      f = GraphTesting.finishm_graph([[1,2],[3,4]])
+      GraphTesting.add_reads_to_nodes(f, [[1,1],[2,1],[3,2]])
+      GraphTesting.make_reads_paired(f)
+      dijkstra = Bio::AssemblyGraphAlgorithms::Dijkstra.new
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(f.graph.nodes[1], :start_is_first)
+      # won't find node 2 because the default finder is single-ended
+      dijkstra.min_distances(f.graph, onode).should == {[1, :start_is_first]=>0, [2, :start_is_first]=>0}
+    end
+
+    it 'should do paired end jumps' do
+      f = GraphTesting.finishm_graph([[1,2],[3,4]])
+      GraphTesting.add_reads_to_nodes(f, [[1,1],[2,1],[3,2],[4,2]])
+      GraphTesting.make_reads_paired(f)
+      dijkstra = Bio::AssemblyGraphAlgorithms::Dijkstra.new
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(f.graph.nodes[1], :start_is_first)
+      finder = Bio::FinishM::PairedEndNeighbourFinder.new(f, 100)
+
+      dijkstra.min_distances(f.graph, onode, :neighbour_finder => finder
+        ).should == {[1, :start_is_first]=>0,
+          [2, :start_is_first]=>0,
+          [3, :end_is_first] => 80.0,
+          [4, :end_is_first] => 80.0}
+    end
+
+    it 'should respect max-nodes' do
+      f = GraphTesting.finishm_graph([[1,2],[2,3],[3,4]])
+      dijkstra = Bio::AssemblyGraphAlgorithms::Dijkstra.new
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(f.graph.nodes[1], :start_is_first)
+      dijkstra.min_distances(f.graph, onode).should == {
+        [1, :start_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [3, :start_is_first]=>10,
+        [4, :start_is_first]=>20,
+        }
+      dijkstra.min_distances(f.graph, onode, :max_nodes => 2).should == {
+        [1, :start_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [3, :start_is_first]=>10,
+        }
+      # TIM - The algorithm has weird behaviour with :max_nodes => 0, as the starting node has distance zero
+      # and so do the first neighbours so technically they tie with the zero-th node found.
+      #dijkstra.min_distances(f.graph, onode, :max_nodes => 0).should == {
+      #  [1, :start_is_first]=>0,
+      #  }
+      dijkstra.min_distances(f.graph, onode, :max_nodes => 3).should == {
+        [1, :start_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [3, :start_is_first]=>10,
+        [4, :start_is_first]=>20,
+        }
+      dijkstra.min_distances(f.graph, onode, :max_nodes => 30).should == {
+        [1, :start_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [3, :start_is_first]=>10,
+        [4, :start_is_first]=>20,
+        }
+    end
+
+    it 'should max-nodes when ignoring directions' do
+      f = GraphTesting.finishm_graph([[1,2],[2,3],[3,4]])
+      dijkstra = Bio::AssemblyGraphAlgorithms::Dijkstra.new
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(f.graph.nodes[1], :start_is_first)
+
+      #dijkstra.min_distances(f.graph, onode, {:max_nodes => 0, :ignore_directions => true}).should == {
+      #  [1, :start_is_first]=>0,
+      #  [1, :end_is_first]=>0,
+      #  }
+      dijkstra.min_distances(f.graph, onode, {:max_nodes => 1, :ignore_directions => true}).should == {
+        [1, :start_is_first]=>0,
+        [1, :end_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [2, :end_is_first]=>0,
+        }
+      dijkstra.min_distances(f.graph, onode, {:max_nodes => 2, :ignore_directions => true}).should == {
+        [1, :start_is_first]=>0,
+        [1, :end_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [2, :end_is_first]=>0,
+        [3, :start_is_first]=>10,
+        [3, :end_is_first]=>10
+        }
+    end
+
+    it 'should be ok with max-nodes when there is a tie' do
+      f = GraphTesting.finishm_graph([[1,2],[1,3]])
+      dijkstra = Bio::AssemblyGraphAlgorithms::Dijkstra.new
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(f.graph.nodes[1], :start_is_first)
+
+      #dijkstra.min_distances(f.graph, onode, {:max_nodes => 0, :ignore_directions => true}).should == {
+      #  [1, :start_is_first]=>0,
+      #  [1, :end_is_first]=>0,
+      #  }
+      dijkstra.min_distances(f.graph, onode, {:max_nodes => 1, :ignore_directions => true}).should == {
+        [1, :start_is_first]=>0,
+        [1, :end_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [2, :end_is_first]=>0,
+        [3, :start_is_first]=>0,
+        [3, :end_is_first]=>0,
+        }
+
+      f = GraphTesting.finishm_graph([[10,1],[1,2],[1,3]])
+      dijkstra = Bio::AssemblyGraphAlgorithms::Dijkstra.new
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(f.graph.nodes[10], :start_is_first)
+      dijkstra.min_distances(f.graph, onode, {:max_nodes => 2, :ignore_directions => true}).should == {
+        [10, :start_is_first]=>0,
+        [10, :end_is_first]=>0,
+        [1, :start_is_first]=>0,
+        [1, :end_is_first]=>0,
+        [2, :start_is_first]=>10,
+        [2, :end_is_first]=>10,
+        [3, :start_is_first]=>10,
+        [3, :end_is_first]=>10,
+        }
+    end
+
+    it 'should not get tripped up on negative distances' do
+      f = GraphTesting.finishm_graph([[1,2],[3,4]])
+      dijkstra = Bio::AssemblyGraphAlgorithms::Dijkstra.new
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(f.graph.nodes[1], :start_is_first)
+      GraphTesting.add_reads_to_nodes(f, [[2,1],[3,2]])
+      GraphTesting.make_reads_paired(f)
+      GraphTesting.set_node_length(f.graph.nodes[2], 1000)
+      finder = Bio::FinishM::PairedEndNeighbourFinder.new(f, 100)
+      dijkstra.min_distances(f.graph, onode, {
+        :max_nodes => 1, :ignore_directions => true, :neighbour_finder => finder
+        }).should == {
+        [1, :start_is_first]=>0,
+        [1, :end_is_first]=>0,
+        [2, :start_is_first]=>0,
+        [2, :end_is_first]=>0,
+        }
+    end
+  end
+end

data/spec/explore_spec.rb

@@ -0,0 +1,29 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio-commandeer'
+
+#Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')
+
+describe "FinishM explore" do
+  it 'should explore just a single but rather complex trail' do
+    data_path = File.join(TEST_DATA_DIR,'explore','1')
+    trails = nil
+    Dir.chdir(data_path) do
+      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} explore --quiet --contigs a.fa --interesting-ends random:end --output-explored-paths - --fasta 2seqs.sammy.fa"
+    end
+    splits = trails.split("\n").to_a.sort
+    splits.length.should == 1024
+    splits[0].match(/>random:end Dead end \/ coverage nodes:(\d),[\d,]+/)[1].should == '1'
+    splits[1023][0...100].should == 'CCTATCCGGTCCCCCTAGAATGTTGATTCCTCCGTCTTCTGATTTCCGTTGGCGGTTCGTATCGGCTCCCGTACAACCGCCGGAATTGAAGTGTACCTTG'
+  end
+
+  it 'should explore when interesting ends is all' do
+    data_path = File.join(TEST_DATA_DIR,'explore','1')
+    trails = nil
+    Dir.chdir(data_path) do
+      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} explore --quiet --contigs a.fa --interesting-ends all --output-explored-paths - --fasta 2seqs.sammy.fa"
+    end
+    splits = trails.split("\n").to_a
+    splits.length.should == 1026
+    splits[0].match(/>random:start Dead end \/ coverage nodes:(\d)/)[1].should == '1'
+  end
+end

data/spec/fluffer_spec.rb

@@ -0,0 +1,155 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+#Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')
+
+describe "Fluffer" do
+  it 'should work with a very straightforward single path' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+    ], [1])
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 100)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1,2], :dead_end]
+      ],
+    ]
+  end
+
+  it 'should work with two starting points' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+      [2,3],
+      [3,4]
+    ], [1,3])
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 100)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1,2,3], :terminal_node]
+      ],
+      [
+        [[3,4], :dead_end]
+      ]
+    ]
+  end
+
+  it 'should work with two starting points and a dead end' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+      [2,3],
+      [3,4],
+      [2,5],
+    ], [1,3])
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 100)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1,2,3], :terminal_node],
+        [[1,2,5], :dead_end],
+      ],
+      [
+        [[3,4], :dead_end]
+      ]
+    ]
+  end
+
+  it 'should respect leash lengths' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+      [2,3],
+      [3,4],
+      [2,5],
+    ], [1,3])
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 5)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1], :beyond_leash_length]
+      ],
+      [
+        [[3], :beyond_leash_length]
+      ]
+    ]
+  end
+
+  it 'should be able to handle missing probes' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+      [2,3],
+      [3,4],
+      [2,5],
+    ], [1,3])
+    finishm_graph.probe_nodes[2] = nil
+    finishm_graph.probe_node_directions[2] = nil
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 5)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1], :beyond_leash_length]
+      ],
+      [
+        [[3], :beyond_leash_length]
+      ],[
+      ]
+    ]
+  end
+
+  it 'should be able to handle missing probes in the middle' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+      [2,3],
+      [3,4],
+      [2,5],
+    ], [1,2,3])
+    finishm_graph.probe_nodes[1] = nil
+    finishm_graph.probe_node_directions[1] = nil
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 5)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1], :beyond_leash_length]
+      ],
+      [
+      ],
+      [
+        [[3], :beyond_leash_length]
+      ]
+    ]
+  end
+
+  it 'should deal with already seen nodes properly' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+      [2,3],
+      [1,3],
+      [3,4]
+    ], [1])
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 100)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1,2,3,4], :dead_end],
+        [[1,3,4], :dead_end],
+      ],
+    ]
+  end
+
+  it 'should mark beyond leash length paths as golden' do
+    finishm_graph = GraphTesting.finishm_graph([
+      [1,2],
+      [2,3],
+      [1,3],
+      [3,4],
+      [4,5],
+    ], [1])
+    fluffer = Bio::AssemblyGraphAlgorithms::Fluffer.new
+    path_sets = fluffer.fluff(finishm_graph, 25)
+    GraphTesting.sorted_fluffers(path_sets).should == [
+      [
+        [[1,2,3], :beyond_leash_length],
+        [[1,3], :beyond_leash_length],
+      ],
+    ]
+  end
+end