finishm 0.0.1

data/spec/spec_helper.rb

@@ -0,0 +1,310 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'priner'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  config.expect_with :rspec do |c|
+    # ...or explicitly enable both
+    c.syntax = [:should, :expect]
+  end
+end
+TEST_DATA_DIR = File.join(File.dirname(__FILE__),'data')
+FINISHM_SCRIPT_PATH = File.join(File.dirname(__FILE__),'..','bin','finishm')
+
+Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm'); Bio::Log::LoggerPlus.new('bio-velvet'); Bio::Log::CLI.configure('bio-velvet')
+
+class GraphTesting
+  def self.emit(arc_pairs)
+    node_id_to_node = {}
+    graph = Bio::Velvet::Graph.new
+    arc_array = Bio::Velvet::Graph::ArcArray.new
+    graph.arcs = arc_array
+    nodes = Bio::Velvet::Graph::NodeArray.new
+    graph.nodes = nodes
+    graph.hash_length = 7
+
+    arc_pairs.each do |node_ids|
+      raise unless node_ids.length == 2
+
+      # Create the nodes if necessary
+      node_ids.each_with_index do |ident|
+        node = node_id_to_node[ident]
+        if node.nil?
+          node = Bio::Velvet::Graph::Node.new
+          node.node_id = ident
+          node_id_to_node[ident] = node
+          node.parent_graph = graph
+          node.length = 10
+          node.ends_of_kmers_of_node = 'A'*node.length
+          node.ends_of_kmers_of_twin_node = 'T'*node.length
+          node.coverages = [5]
+          node.short_reads = Bio::Velvet::Graph::NodedReadArray.new
+        end
+        nodes[ident] = node
+      end
+
+      # Create the arc itself
+      arc = Bio::Velvet::Graph::Arc.new
+      arc.begin_node_id = node_ids[0]
+      arc.end_node_id = node_ids[1]
+      arc.begin_node_direction = true
+      arc.end_node_direction = true
+      arc_array.push arc
+    end
+
+    return graph
+  end
+
+  def self.emit_ss(arc_pairs, start_node_id, stop_node_id=1)
+    graph = emit(arc_pairs)
+    initial = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+    initial.node = graph.nodes[start_node_id]
+    initial.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+    initial_path = Bio::Velvet::Graph::OrientedNodeTrail.new
+    initial_path.add_oriented_node initial
+    terminal = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+    terminal.node = graph.nodes[stop_node_id]
+    terminal.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+
+    return graph, initial_path, terminal
+  end
+
+  def self.finishm_graph(arc_pairs, probes=[])
+    graph = emit(arc_pairs)
+    finishm_graph = Bio::FinishM::ProbedGraph.new
+    finishm_graph.graph = graph
+    finishm_graph.probe_nodes = probes.collect{|probe| graph.nodes[probe]}
+    finishm_graph.probe_node_directions = probes.collect{true}
+
+    return finishm_graph
+  end
+
+  def self.sorted_paths(paths)
+    paths.collect do |path|
+      path.collect{|n| n.node_id}
+    end.sort
+  end
+
+  def self.sorted_array_of_paths(path_array)
+    path_array.collect do |paths|
+      paths.collect do |path|
+        path.collect{|n| n.node_id}
+      end.sort
+    end
+  end
+
+  def self.sorted_fluffers(path_array)
+    path_array.collect do |fluffer_path_set|
+      paths_and_fates = []
+      fluffer_path_set.each_with_index do |path, i|
+        paths_and_fates.push [
+          path.collect{|n| n.node_id},
+          fluffer_path_set.fates[i]
+        ]
+      end
+      paths_and_fates.sort
+    end
+  end
+
+  def self.sorted_fwd_paths(paths)
+    paths.collect! do |path|
+      if path[0].node_id > path[-1].node_id
+        path.reverse
+      else
+        path
+      end
+    end
+    paths.sort do |p1,p2|
+      p1.collect{|o|o.node_id} <=> p2.collect{|o|o.node_id}
+    end
+  end
+
+  def self.sorted_fwd_shorthand_paths(paths)
+    sorted_fwd_paths(paths).collect do |path|
+      path.to_shorthand
+    end
+  end
+
+  def self.emit_paths(paths)
+    arcs = []
+    paths.each do |path|
+      (0...(path.length-1)).each do |i|
+        arcs << [path[i],path[i+1]]
+      end
+    end
+    graph = emit(arcs)
+
+    return graph, paths.collect do |path|
+      path.collect do |node_id|
+        onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+        onode.node = graph.nodes[node_id]
+        onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+        onode
+      end
+    end
+  end
+
+  def self.emit_otrails(paths)
+    graph, paths2 = emit_paths(paths)
+    return graph, paths2.collect do |path|
+      trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+      path.each do |onode|
+        trail.add_oriented_node onode
+      end
+      trail
+    end
+  end
+
+  def self.emit_printer_connection(graph, ref, variants)
+    conn = Bio::AssemblyGraphAlgorithms::ContigPrinter::Connection.new
+    conn.reference_path = ref.collect do |node_id|
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+      onode.node = graph.nodes[node_id]
+      onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+      onode
+    end
+    conn.variants = variants.collect do |variant|
+      var = Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant.new
+
+      start = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+      start.node = graph.nodes[variant[0]]
+      start.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+      var.reference_oriented_node_before_variant = start
+
+      stop = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+      stop.node = graph.nodes[variant[1]]
+      stop.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+      var.reference_oriented_node_after_variant = stop
+
+      var.variation_path = []
+      variant[2...variant.length].each do |node_id|
+        onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+        onode.node = graph.nodes[node_id]
+        onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+        var.variation_path.push onode
+      end
+
+      var
+    end
+
+    return conn.comparable
+  end
+
+  def self.make_onodes(graph, array)
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    array = array.split(',') if array.kind_of?(String)
+
+    array.each do |e|
+      raise unless e.kind_of?(String)
+      node_i = e.to_i
+      node_str = node_i.to_s
+      node = graph.nodes[node_i]
+      dir = nil
+      if e[node_str.length] == 's'
+        dir = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+      elsif e[node_str.length] == 'e'
+        dir = dir = Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST
+      else
+        raise
+      end
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
+      onode.node = node
+      onode.first_side = dir
+      trail.add_oriented_node onode
+    end
+
+    return trail
+  end
+
+  def self.add_noded_reads(graph, paths)
+    paths.each_with_index do |path, i|
+      path.each do |node_id|
+        node = graph.nodes[node_id]
+        noded_read = Bio::Velvet::Graph::NodedRead.new
+        noded_read.read_id = i
+
+        node.short_reads ||= Bio::Velvet::Graph::NodedReadArray.new
+        node.short_reads.push noded_read
+      end
+    end
+  end
+
+  def self.add_reads_to_nodes(finishm_graph, arrays)
+    node = nil
+    read_id_to_node_id = DummyReadToNode.new
+    arrays.each_with_index do |node_and_reads|
+      node_and_reads.each_with_index do |node_or_read, i|
+        if i==0
+          node = finishm_graph.graph.nodes[node_or_read]
+        else
+          noded_read = Bio::Velvet::Graph::NodedRead.new
+          noded_read.read_id = node_or_read
+          noded_read.direction = true
+          noded_read.start_coord = 0
+          noded_read.offset_from_start_of_node = 0
+          node.short_reads ||= Bio::Velvet::Graph::NodedReadArray.new
+          node.short_reads.push noded_read
+
+          read_id_to_node_id[node_or_read] ||= []
+          read_id_to_node_id[node_or_read].push node.node_id
+        end
+      end
+    end
+
+    # set all nodes without reads too
+    finishm_graph.graph.nodes.each do |node|
+      read_id_to_node_id[node.node_id] ||= []
+    end
+
+    finishm_graph.read_to_nodes = read_id_to_node_id
+
+    # Make all reads single by default
+    finishm_graph.velvet_sequences = DummySequenceStore.new
+  end
+
+  def self.make_reads_paired(finishm_graph)
+    range = (finishm_graph.read_to_nodes.keys.min..finishm_graph.read_to_nodes.keys.max)
+    finishm_graph.velvet_sequences = DummySequenceStore.new(range)
+  end
+
+  def self.set_node_length(node, length)
+    node.ends_of_kmers_of_node = 'A'*length
+    node.ends_of_kmers_of_twin_node = 'T'*length
+  end
+end
+
+class DummySequenceStore
+  def initialize(pair_range=nil)
+    @hash = {}
+
+    # make pairs if desired
+    unless pair_range.nil?
+      a = pair_range.to_a
+      raise "need even number of reads in pair_range" unless a.length % 2 == 0
+      a.each_with_index do |e, i|
+        next if i % 2 == 0 #ignore even-numbered entries
+        @hash[i] = i+1
+        @hash[i+1] = i
+      end
+    end
+  end
+
+  def pair_id(read_id)
+    @hash[read_id]
+  end
+end
+
+class DummyReadToNode < Hash
+end
+
+
+class Util
+  def self.revcom(seq)
+    Bio::Sequence::NA.new(seq).reverse_complement.to_s.upcase
+  end
+end

data/spec/velvet_graph_sequence_extractor_spec.rb

@@ -0,0 +1,80 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio'
+class Util
+  def self.revcom(seq)
+    Bio::Sequence::NA.new(seq).reverse_complement.to_s.upcase
+  end
+end
+
+describe "velvet graph walker" do
+  it 'should calculate trail sequences' do
+    graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
+    hash_length = 31
+    # Make sure we are on the same page
+    graph.arcs.length.should eq(4)
+    graph.nodes.length.should eq(4)
+    nodes = graph.nodes
+
+    walker = Bio::AssemblyGraphAlgorithms::LazyGraphWalker.new
+
+    Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')
+
+    # sequenceChop.pl read1.fa 1 258
+    exp = 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG'
+    walker.trail_sequence(graph, [nodes[1]]).should eq(exp)
+
+    # sequenceChop.pl read1.fa 1 287
+    exp = 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAA'
+    walker.trail_sequence(graph, [nodes[1],nodes[2]]).should eq(exp)
+
+    lambda {walker.trail_sequence(graph, [nodes[1],nodes[2],nodes[3]]).should raise_error(Bio::AssemblyGraphAlgorithms::GraphWalkingException)} #Nodes 2 and 3 don't share an arc
+
+    # read1.fa all
+    exp = 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG'
+    walker.trail_sequence(graph, [nodes[1],nodes[2],nodes[4]]).should eq(exp)
+
+    # reverseFasta.pl read1.fa
+    exp = 'CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG'
+    walker.trail_sequence(graph, [nodes[4],nodes[2],nodes[1]]).should eq(exp)
+
+    lambda {walker.trail_sequence(graph, [nodes[2],nodes[4],nodes[3]]).should raise_error(Bio::AssemblyGraphAlgorithms::GraphWalkingException)} #share arcs, but in the wrong direction (2 and 3 both go to the start of 4)
+
+    walker.trail_sequence(graph, []).should eq('')
+  end
+
+  it 'should calculate something similar in reverse' do
+    # ..../spec/data/velvet_test_trails_reverse$ reverseFasta.pl ../velvet_test_trails/reads.fa >reads_reversed.fa
+    graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails_reverse','Assem','LastGraph')
+    hash_length = 31
+    # Make sure we are on the same page
+    graph.arcs.length.should eq(4)
+    graph.nodes.length.should eq(4)
+    nodes = graph.nodes
+
+    walker = Bio::AssemblyGraphAlgorithms::LazyGraphWalker.new
+
+    Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('info'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')
+
+    # sequenceChop.pl read1.fa 1 258
+    exp = Util.revcom 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG'
+    walker.trail_sequence(graph, [nodes[3]]).should eq(exp)
+
+    # sequenceChop.pl read1.fa 1 287
+    exp = 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAA'
+    walker.trail_sequence(graph, [nodes[3],nodes[2]]).should eq(exp)
+
+    lambda {walker.trail_sequence(graph, [nodes[3],nodes[2],nodes[4]]).should raise_error(Bio::AssemblyGraphAlgorithms::GraphWalkingException)} #Nodes 2 and 3 don't share an arc
+
+    # read1.fa all
+    exp = 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG'
+    walker.trail_sequence(graph, [nodes[3],nodes[2],nodes[1]]).should eq(exp)
+
+    # reverseFasta.pl read1.fa
+    exp = 'CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG'
+    walker.trail_sequence(graph, [nodes[1],nodes[2],nodes[3]]).should eq(exp)
+
+    lambda {walker.trail_sequence(graph, [nodes[2],nodes[1],nodes[4]]).should raise_error(Bio::AssemblyGraphAlgorithms::GraphWalkingException)} #share arcs, but in the wrong direction (2 and 3 both go to the start of 4)
+
+    walker.trail_sequence(graph, []).should eq('')
+  end
+end

data/spec/visualise_spec.rb

@@ -0,0 +1,105 @@
+
+require 'bio-commandeer'
+require 'spec_helper'
+
+describe 'finishm visualise' do
+  path_to_script = File.join(File.dirname(__FILE__),'..','bin','finishm visualise')
+
+  it 'should visualise an entire graph' do
+    command = "#{path_to_script} --quiet --already-assembled-velvet-directory #{TEST_DATA_DIR}/visualise/1 --assembly-dot /dev/stdout"
+    stdout = Bio::Commandeer.run(command)
+    stdout.should == <<END_OF_DOT
+digraph G {
+	graph [overlap=scale];
+	node [label="\\N"];
+	graph [bb="0,0,1533,556"];
+	1 [label=n1_length527_coverage21, pos="142,389", width="3.9444", height="0.51389"];
+	2 [label=n2_length264_coverage33, pos="142,463", width="3.9444", height="0.51389"];
+	3 [label=n3_length227_coverage62, pos="397,537", width="3.9444", height="0.51389"];
+	4 [label=n4_length169_coverage16, pos="1077,167", width="3.9444", height="0.51389"];
+	5 [label=n5_length155_coverage32, pos="482,463", width="3.9444", height="0.51389"];
+	6 [label=n6_length11_coverage71, pos="549,389", width="3.7778", height="0.51389"];
+	7 [label=n7_length87_coverage29, pos="781,167", width="3.7778", height="0.51389"];
+	8 [label=n8_length102_coverage16, pos="1382,315", width="3.9444", height="0.51389"];
+	9 [label=n9_length117_coverage36, pos="1231,241", width="3.9444", height="0.51389"];
+	10 [label=n10_length89_coverage71, pos="617,241", width="3.9444", height="0.51389"];
+	11 [label=n11_length103_coverage34, pos="441,167", width="4.1111", height="0.51389"];
+	12 [label=n12_length11_coverage41, pos="932,93", width="3.9444", height="0.51389"];
+	13 [label=n13_length155_coverage38, pos="790,463", width="4.1111", height="0.51389"];
+	14 [label=n14_length169_coverage20, pos="1385,167", width="4.1111", height="0.51389"];
+	15 [label=n15_length82_coverage21, pos="1080,315", width="3.9444", height="0.51389"];
+	16 [label=n16_length103_coverage35, pos="617,315", width="4.1111", height="0.51389"];
+	17 [label=n17_length264_coverage19, pos="224,315", width="4.1111", height="0.51389"];
+	18 [label=n18_length87_coverage36, pos="774,19", width="3.9444", height="0.51389"];
+	2 -> 1 [pos="e,142,407.67 142,444.33 142,436.26 142,426.65 142,417.71"];
+	1 -> 17 [color=blue, pos="e,203.6,333.41 162.69,370.33 172.77,361.23 185.04,350.16 195.95,340.32"];
+	3 -> 2 [pos="e,200.37,479.94 338.82,520.12 300.52,509 250.24,494.41 210.09,482.76"];
+	3 -> 17 [arrowhead=none, pos="368.49,518.69 355.51,509.11 340.88,496.39 331,482 301.25,438.66 323.22,413.01 293,370 282.78,355.46 267.66,342.8 254.17,333.31"];
+	3 -> 5 [color=blue, pos="e,460.85,481.41 418.45,518.33 429,509.14 441.86,497.94 453.25,488.03"];
+	3 -> 13 [color=blue, pos="e,708.14,478.41 477.95,521.76 541.96,509.7 631.35,492.87 698.05,480.31"];
+	4 -> 12 [pos="e,967.36,111.04 1041.5,148.9 1021.9,138.87 997.28,126.31 976.37,115.64"];
+	9 -> 4 [pos="e,1114.2,184.88 1193.7,223.09 1172.5,212.9 1145.8,200.05 1123.3,189.22"];
+	5 -> 6 [pos="e,532.33,407.41 498.91,444.33 506.98,435.41 516.78,424.59 525.56,414.89"];
+	6 -> 11 [arrowhead=none, pos="504.23,371.47 487.67,362.71 470.41,350.41 460,334 430.38,287.31 434.2,218.23 438.18,185.5"];
+	6 -> 16 [pos="e,600.08,333.41 566.16,370.33 574.36,361.41 584.3,350.59 593.21,340.89"];
+	13 -> 6 [pos="e,604.18,405.94 734.1,445.84 698.24,434.82 651.53,420.48 614,408.96"];
+	7 -> 12 [arrowhead=none, pos="817.55,149.09 841.12,137.54 871.66,122.57 895.26,111"];
+	10 -> 7 [pos="e,741.67,184.75 656.7,223.09 679.46,212.82 708.22,199.84 732.33,188.96"];
+	8 -> 9 [pos="e,1267.7,259 1345.4,297.09 1324.8,286.98 1298.9,274.26 1276.9,263.49"];
+	9 -> 14 [pos="e,1347.5,185 1268.3,223.09 1289.4,212.94 1316,200.15 1338.5,189.34"];
+	15 -> 9 [pos="e,1194.3,259 1116.6,297.09 1137.2,286.98 1163.1,274.26 1185.1,263.49"];
+	10 -> 18 [arrowhead=none, pos="617.51,222.38 618.76,202.73 622.88,171.44 636,148 662.91,99.923 713.93,59.391 745.83,37.207"];
+	16 -> 10 [pos="e,617,259.67 617,296.33 617,288.26 617,278.65 617,269.71"];
+	10 -> 11 [color=blue, pos="e,483.42,184.84 574.84,223.28 550.21,212.92 518.92,199.76 492.79,188.78"];
+	12 -> 18 [pos="e,812.17,36.876 893.75,75.087 872,64.898 844.57,52.052 821.45,41.224"];
+	14 -> 12 [pos="e,1020.7,107.49 1295,152.29 1218.6,139.82 1109.3,121.97 1030.6,109.11"];
+}
+END_OF_DOT
+  end
+
+  it 'should visualise particular nodes of interest' do
+    command = "#{path_to_script} --quiet --already-assembled-velvet-directory #{TEST_DATA_DIR}/visualise/1 --assembly-dot /dev/stdout --node-ids 1,17 --leash-length 300"
+    stdout = Bio::Commandeer.run(command)
+    stdout.should == <<END_OF_DOT
+digraph G {
+	graph [overlap=scale];
+	node [label="\\N"];
+	graph [bb="0,0,375,260"];
+	1 [label=n1_length527_coverage21, color=red, pos="142,93", width="3.9444", height="0.51389"];
+	2 [label=n2_length264_coverage33, pos="142,167", width="3.9444", height="0.51389"];
+	3 [label=n3_length227_coverage62, pos="227,241", width="3.9444", height="0.51389"];
+	17 [label=n17_length264_coverage19, color=red, pos="227,19", width="4.1111", height="0.51389"];
+	2 -> 1 [pos="e,142,111.67 142,148.33 142,140.26 142,130.65 142,121.71"];
+	1 -> 17 [color=blue, pos="e,205.85,37.411 163.45,74.327 174,65.143 186.86,53.943 198.25,44.029"];
+	3 -> 2 [pos="e,163.15,185.41 205.55,222.33 195,213.14 182.14,201.94 170.75,192.03"];
+	3 -> 17 [arrowhead=none, pos="259.08,222.98 272.15,213.77 285.85,201.26 293,186 314.11,140.92 314.11,119.08 293,74 285.91,58.872 272.4,46.454 259.43,37.27"];
+}
+END_OF_DOT
+  end
+
+  it 'should visualise --probe-names-file' do
+    Tempfile.open('testing') do |t|
+      t.puts '14_1'
+      t.puts '15_1'
+      t.close
+      Tempfile.open('testing_svg') do |svg_tmp|
+        command = "#{path_to_script} --quiet --fasta #{TEST_DATA_DIR}/wander/1/random1.sammy.fa --assembly-dot /dev/stdout --probe-names-file #{t.path}"
+        stdout = Bio::Commandeer.run(command)
+        stdout.match(/^digraph G/).nil?.should == false
+        stdout.match(/n1_length947_coverage21/).nil?.should == false
+      end
+    end
+  end
+
+  it 'should fail to visualise when --probe-names-file has bad entries' do
+    Tempfile.open('testing') do |t|
+      t.puts '14_1'
+      t.puts '15_1not-a-read'
+      t.close
+      Tempfile.open('testing_svg') do |svg_tmp|
+        command = "#{path_to_script} --quiet --fasta #{TEST_DATA_DIR}/wander/1/random1.sammy.fa --assembly-dot /dev/stdout --probe-names-file #{t.path}"
+        expect{Bio::Commandeer.run(command)}.to raise_error
+      end
+    end
+  end
+end