finishm 0.0.1

data/spec/all_orfs_spec.rb

@@ -0,0 +1,443 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'tempfile'
+
+#Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm'); Bio::Log::CLI.configure('bio-velvet')
+
+class GraphTesting
+  def self.sorted_path_results(paths, forwards=true)
+    paths.sort_by{|path| path.collect{|n| n.node_id}}.collect do |path|
+      forwards ? path.fwd_orfs_result : path.twin_orfs_result
+    end
+  end
+
+  def self.markers(start_positions, stop_positions)
+    [start_positions, stop_positions].collect do |positions|
+      positions.collect do |pos|
+        marker = Bio::AssemblyGraphAlgorithms::AllOrfsFinder::Marker.new
+        marker.position_in_trail = pos
+        marker
+      end
+    end
+  end
+
+  def self.sorted_marker_pair_positions(pair_array)
+    pair_array.collect do |pair|
+      pair.collect{|m| m.position_in_trail}
+    end.sort
+  end
+
+  def self.marker_positions(markers)
+    markers.collect{|m| m.position_in_trail}
+  end
+
+  def self.sorted_marker_pair_node_positions(pair_array)
+    pair_array.sort_by do |pair|
+      pair.collect{|m| m.position_in_trail}
+    end.collect do |pair|
+      pair.collect{|m| [m.node.node_id, m.position_in_node]}
+    end
+  end
+
+  def self.marker_node_positions(markers)
+    markers.collect do |m|
+      [m.node.node_id, m.position_in_node]
+    end
+  end
+end
+
+describe "AllOrfs" do
+
+  it 'should find a hello world ORF' do
+    graph, = GraphTesting.emit_otrails([
+      [1,2,3]
+      ])
+    graph.nodes[1].ends_of_kmers_of_node = 'TAAATGGAAA' #stop codon 'TAA', start codon 'ATG'
+    graph.nodes[3].ends_of_kmers_of_node = 'AAAAAAATAA' #stop codon 'TAA'
+    initial_path = GraphTesting.make_onodes(graph, %w(1s))
+
+    orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+    problems = orfer.find_all_problems(graph, [initial_path])
+    #pp problems
+
+    paths = orfer.find_orfs_from_problems(problems)
+    #pp paths
+    GraphTesting.sorted_paths(paths.trails).should == [
+      [1,2,3]
+      ]
+    res = paths.trails[0].fwd_orfs_result
+    GraphTesting.sorted_marker_pair_positions(res.start_stop_pairs).should == [
+      [6,30]
+      ]
+    GraphTesting.sorted_marker_pair_node_positions(res.start_stop_pairs).should == [
+      [[1,6],[3,10]]
+      ]
+    res.initial_start_markers.should == []
+    GraphTesting.marker_positions(res.initial_stop_markers).should == [3]
+    GraphTesting.marker_node_positions(res.initial_stop_markers).should == [[1,3]]
+    res.final_start_markers.should == []
+  end
+
+  it 'should find a hello world ORF in twin direction' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,3]
+      ])
+    graph.nodes[1].ends_of_kmers_of_twin_node = 'TTTAGTTTTT' # stop codon 'TAG'
+    graph.nodes[2].ends_of_kmers_of_twin_node = 'TAAATGTTTT' # stop codon 'TAA', start codon 'ATG'
+    initial_path = GraphTesting.make_onodes(graph, %w(1s))
+
+    orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+    problems = orfer.find_all_problems(graph, [initial_path])
+    #pp problems
+
+    paths = orfer.find_orfs_from_problems(problems)
+    #pp paths
+    GraphTesting.sorted_paths(paths.trails).should == [
+      [1,2,3]
+      ]
+    res = paths.trails[0].twin_orfs_result
+    GraphTesting.sorted_marker_pair_positions(res.start_stop_pairs).should == [
+      [16,25]
+      ]
+    GraphTesting.sorted_marker_pair_node_positions(res.start_stop_pairs).should == [
+      [[2,6],[1,5]]
+      ]
+    res.initial_start_markers.should == []
+    GraphTesting.marker_positions(res.initial_stop_markers).should == [13]
+    GraphTesting.marker_node_positions(res.initial_stop_markers).should == [[2,3]]
+    res.final_start_markers.should == []
+  end
+
+  it 'should find ORFs over a bubble' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [1,3],
+      [2,4],
+      [3,4]
+      ])
+    graph.nodes[1].ends_of_kmers_of_node = 'TAAATGGAAA' # stop codon 'TAA', start 'ATG'
+    graph.nodes[2].ends_of_kmers_of_node = 'C'
+    graph.nodes[3].ends_of_kmers_of_node = 'A'
+    graph.nodes[4].ends_of_kmers_of_node = 'AAATTAAAAA' # stop 'TAA'
+    initial_path = GraphTesting.make_onodes(graph, %w(1s))
+
+    orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+    problems = orfer.find_all_problems(graph, [initial_path])
+    #pp problems
+    paths = orfer.find_orfs_from_problems(problems)
+    #pp paths
+    GraphTesting.sorted_paths(paths.trails).should == [
+      [1,2,4],
+      [1,3,4]
+      ]
+    res = GraphTesting.sorted_path_results(paths.trails, true) # forward direction
+    res.collect{|result| GraphTesting.sorted_marker_pair_positions(result.start_stop_pairs)}.should == [
+      [[6,18]],
+      [[6,18]]
+      ]
+    res.collect{|result| result.final_start_markers}.should == [[],[]]
+    res.collect{|result| result.initial_start_markers}.should == [[],[]]
+    res.collect{|result| GraphTesting.marker_positions(result.initial_stop_markers)}.should == [
+      [3],
+      [3]
+      ]
+    res.collect{|result| GraphTesting.marker_node_positions(result.initial_stop_markers)}.should == [
+      [[1,3]],
+      [[1,3]]
+      ]
+  end
+
+  it 'should respect phase along each trail' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [1,3],
+      [2,4],
+      [3,4]
+      ])
+    graph.nodes[1].ends_of_kmers_of_node = 'TAAATGGAAA' # stop 'TAA', start 'ATG'
+    graph.nodes[2].ends_of_kmers_of_node = 'C'
+    graph.nodes[3].ends_of_kmers_of_node = 'AAA'
+    graph.nodes[4].ends_of_kmers_of_node = 'AAATTAGAAA' # stop 'TAG'
+    initial_path = GraphTesting.make_onodes(graph, %w(1s))
+
+    orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+    problems = orfer.find_all_problems(graph, [initial_path])
+    #pp problems
+    paths = orfer.find_orfs_from_problems(problems)
+    #pp paths
+    GraphTesting.sorted_paths(paths.trails).should == [
+      [1,2,4],
+      [1,3,4]
+      ]
+    res = GraphTesting.sorted_path_results(paths.trails, true) # forwards direction
+    res.collect{|result| GraphTesting.sorted_marker_pair_positions(result.start_stop_pairs)}.should == [
+      [[6,18]],
+      []
+      ]
+    GraphTesting.sorted_marker_pair_node_positions(res[0].start_stop_pairs).should == [
+      [[1,6],[4,7]]
+      ]
+    res.collect{|result| GraphTesting.marker_positions(result.final_start_markers)}.should == [
+      [],
+      [6]
+      ]
+    GraphTesting.marker_node_positions(res[1].final_start_markers).should == [
+      [1,6]
+      ]
+    res.collect{|result| GraphTesting.marker_positions(result.initial_stop_markers)}.should ==[
+      [3],
+      [3,20]
+      ]
+    res.collect{|result| GraphTesting.marker_node_positions(result.initial_stop_markers)}.should == [
+      [[1,3]],
+      [[1,3],[4,7]]
+      ]
+    res.collect{|result| result.initial_start_markers}.should == [[],[]]
+  end
+
+
+  it 'should respect terminal nodes' do
+    fail '#todo'
+  end
+
+  it 'should respect minimum orf length' do
+    fail '#todo'
+  end
+
+  it 'should respect max gapfill paths' do
+    fail '#todo'
+  end
+
+  it 'should respect max cycles' do
+    fail '#todo'
+  end
+
+  describe 'search_for_codons' do
+    it 'should report end positions for codons starting in first node of trail' do
+      graph, otrails = GraphTesting.emit_otrails([[1,2]])
+      graph.nodes[1].ends_of_kmers_of_node = 'AAATGAAAAA' # start codon 'ATG', stop codon 'TGA'
+      graph.nodes[1].ends_of_kmers_of_twin_node = 'TTTTTAACTT' # stop codon 'TAA'
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      fwd_res, twin_res = orfer.search_for_codons(otrails[0])
+      fwd_res.start_markers.collect{|m| m.position_in_node}.should == [5]
+      fwd_res.stop_markers.collect{|m| m.position_in_node}.should == [6]
+      fwd_res.start_markers.all?{|n| n.node.node_id == 1}.should == true
+      fwd_res.stop_markers.all?{|n| n.node.node_id == 1}.should == true
+      twin_res.start_markers.should == []
+      twin_res.stop_markers.collect{|m| m.position_in_node}.should == [7]
+      twin_res.start_markers.all?{|n| n.node.node_id == 1}.should == true
+      twin_res.stop_markers.all?{|n| n.node.node_id == 1}.should == true
+    end
+
+    it 'should work on single-node trail' do
+      graph, otrails = GraphTesting.emit([[1,2]])
+      graph.nodes[1].ends_of_kmers_of_node = 'AAATAATAAA' # stop codon 'TAA'
+      graph.nodes[1].ends_of_kmers_of_twin_node = 'TTGATGTTTT' # start codon 'ATG', stop codon 'TGA'
+      otrail = Bio::Velvet::Graph::OrientedNodeTrail.new
+      otrail.add_node graph.nodes[1], Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      fwd_res, twin_res = orfer.search_for_codons(otrail)
+      fwd_res.start_markers.should == []
+      fwd_res.stop_markers.collect{|m| m.position_in_node}.should == [6,9]
+      twin_res.start_markers.collect{|m| m.position_in_node}.should == [6]
+      twin_res.stop_markers.collect{|m| m.position_in_node}.should == [4]
+    end
+  end
+
+  describe 'get_overlap_sequences' do
+    it 'should traverse trail to get enough sequence' do
+      graph, otrails = GraphTesting.emit_otrails([[1,2]])
+      graph.nodes[2].ends_of_kmers_of_node = 'G'*10 # Second node is sequence of G's
+      graph.nodes[2].ends_of_kmers_of_twin_node = 'C'*10
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      orfer.get_overlap_sequences(otrails[0], 3).should == [
+        'AAGG',
+        'CCTT'
+        ]
+    end
+
+    it 'should look across multiple nodes if necessary' do
+      graph, otrails = GraphTesting.emit_otrails([[1,2,3]])
+      graph.nodes[2].ends_of_kmers_of_node = 'G' # Second node is single G
+      graph.nodes[2].ends_of_kmers_of_twin_node = 'C'
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      orfer.get_overlap_sequences(otrails[0], 4).should == [
+        'AAAGAA',
+        'TTCTTT'
+        ]
+    end
+
+    it 'should handle a short initial node' do
+      graph, otrails = GraphTesting.emit_otrails([[1,2]])
+      graph.nodes[1].ends_of_kmers_of_node = 'C' # First node is single C
+      graph.nodes[1].ends_of_kmers_of_twin_node = 'G'
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      orfer.get_overlap_sequences(otrails[0], 4).should == [
+        'CAAA',
+        'TTTG'
+        ]
+    end
+
+    it 'should be able to work back from end of trail' do
+      graph, otrails = GraphTesting.emit_otrails([[1,2,3]])
+      graph.nodes[2].ends_of_kmers_of_node = 'C'
+      graph.nodes[2].ends_of_kmers_of_twin_node = 'G'
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      orfer.get_overlap_sequences(otrails[0], 5, true).should == [
+        'AAACAAAA',
+        'TTTTGTTT'
+        ]
+    end
+  end
+
+  describe 'get_sequences' do
+    it 'should get forward and twin sequences of a node alone' do
+      graph = GraphTesting.emit([[1,2]])
+      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new graph.nodes[1], true
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      orfer.get_sequences(onode).should == [
+        'A'*10,
+        'T'*10
+        ]
+    end
+  end
+
+  describe 'word_search' do
+    it 'should report end position of words within strings' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      orfer.word_search('Hello', ['lo'], 2).should == {
+        'lo' => [5]
+        }
+      orfer.word_search('Agitate, infiltrate', ['ate', 'lat'], 3).should == {
+        'ate' => [7,19]
+        }
+    end
+  end
+
+  describe 'orfs_from_start_stop_markers' do
+    it 'should work when there are no orfs' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      res = orfer.orfs_from_start_stop_markers([],[],0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      res.start_stop_pairs.should == []
+      res.initial_start_markers.should == []
+      res.initial_stop_markers.should == []
+      res.final_start_markers.should == []
+    end
+
+    it 'should skip an orf before first stop' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      start, stop = GraphTesting.markers [0],[6]
+      res = orfer.orfs_from_start_stop_markers(start,stop,0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      res.start_stop_pairs == []
+      GraphTesting.marker_positions(res.initial_start_markers).should == [0]
+      GraphTesting.marker_positions(res.initial_stop_markers).should == [6]
+      res.final_start_markers.should == []
+    end
+
+    it 'should find an orf after a stop' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      start, stop = GraphTesting.markers [6], [0,9]
+      res = orfer.orfs_from_start_stop_markers(start,stop,0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      GraphTesting.sorted_marker_pair_positions(res.start_stop_pairs).should == [[6,9]]
+      res.initial_start_markers.should == []
+      GraphTesting.marker_positions(res.initial_stop_markers).should == [0]
+      res.final_start_markers.should == []
+    end
+
+    it 'should work for one orf in 2 frames' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      start, stop = GraphTesting.markers([3,5],[0,2,6,11])
+      res = orfer.orfs_from_start_stop_markers(start, stop, 0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      GraphTesting.sorted_marker_pair_positions(res.start_stop_pairs).should == [[3,6],[5,11]]
+      res.initial_start_markers.should == []
+      GraphTesting.marker_positions(res.initial_stop_markers).should == [0,2]
+      res.final_start_markers.should == []
+    end
+
+    it 'should work with unclosed orfs' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      start, stop = GraphTesting.markers([],[7])
+      res = orfer.orfs_from_start_stop_markers(start,stop,0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      res.start_stop_pairs.should == []
+      res.initial_start_markers.should == []
+      GraphTesting.marker_positions(res.initial_stop_markers).should == [7]
+      res.final_start_markers.should == []
+
+      start, stop = GraphTesting.markers([7],[])
+      res = orfer.orfs_from_start_stop_markers(start,stop,0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      res.start_stop_pairs.should == []
+      GraphTesting.marker_positions(res.initial_start_markers).should == [7]
+      res.initial_stop_markers.should == []
+      res.final_start_markers.should == []
+    end
+
+    it 'should work with 3 orfs' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      start, stop = GraphTesting.markers([8,14,20],[2,11,17,44])
+      res = orfer.orfs_from_start_stop_markers(start,stop,0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      GraphTesting.sorted_marker_pair_positions(res.start_stop_pairs).should == [[8,11],[14,17],[20,44]]
+      res.initial_start_markers.should == []
+      GraphTesting.marker_positions(res.initial_stop_markers).should == [2]
+      res.final_start_markers.should == []
+    end
+
+    it 'should work with an internal start codon' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      start, stop = GraphTesting.markers([8,14,20],[5,17,44])
+      res = orfer.orfs_from_start_stop_markers(start,stop,0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      GraphTesting.sorted_marker_pair_positions(res.start_stop_pairs).should == [[8,17],[20,44]]
+      res.initial_start_markers.should == []
+      GraphTesting.marker_positions(res.initial_stop_markers).should == [5]
+      res.final_start_markers.should == []
+    end
+
+    it 'should find first stop codon in a frame before an orf and first start after' do
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      start, stop = GraphTesting.markers([7,13,19],[1,4,10])
+      res = orfer.orfs_from_start_stop_markers(start, stop, 0)
+      res.kind_of?(Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult).should == true
+      GraphTesting.sorted_marker_pair_positions(res.start_stop_pairs).should == [[7,10]]
+      GraphTesting.marker_positions(res.initial_stop_markers).should == [1]
+      GraphTesting.marker_positions(res.final_start_markers).should == [13]
+    end
+  end
+
+  describe 'orf_sequences_from_trails' do
+    it 'should return orf sequences for a hello world orf' do
+      graph = GraphTesting.emit([
+        [1,2],
+        [2,3]
+        ])
+      graph.nodes[1].ends_of_kmers_of_node = 'TAAATGGAAA' #stop codon 'TAA', start codon 'ATG'
+      graph.nodes[3].ends_of_kmers_of_node = 'AAAAAAATAA' #stop codon 'TAA'
+      initial_path = GraphTesting.make_onodes(graph, %w(1s))
+
+      orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
+      problems = orfer.find_all_problems(graph, [initial_path])
+      #pp problems
+
+      paths = orfer.find_orfs_from_problems(problems)
+      #pp paths
+      orfer.orf_sequences_from_trails(paths.trails).should == {
+        '(1s:6),2s,(3s:10)' => 'ATGGAAAAAAAAAAAAAAAAAAAATAA',
+        '1s,2s,3s' => 'T'*30,
+        ',(1s:3)' => 'TAA'
+        }
+    end
+  end
+end

data/spec/assemble_spec.rb

@@ -0,0 +1,186 @@
+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 assemble" do
+  it 'should assemble something easy' do
+    data_path = File.join(TEST_DATA_DIR,'explore','1')
+    trails = nil
+    Dir.chdir(data_path) do
+      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} assemble --quiet --output-contigs /dev/stdout --assemble-from '1e' --fasta 2seqs.sammy.fa"#, :log => log
+    end
+    splits = trails.split("\n")
+    splits.length.should == 2
+
+    splits[0].should == ">1e"
+    splits[1][0..60].should == 'TATCCGGTCCCCCTAGAATGTTGATTCCTCCGTCTTCTGATTTCCGTTGGCGGTTCGTATC'
+    splits[1].length.should == 613
+  end
+
+  it 'should output a pathspec' do
+    data_path = File.join(TEST_DATA_DIR,'explore','1')
+    trails = nil
+    Dir.chdir(data_path) do
+      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} assemble --quiet --output-pathspec --output-contigs /dev/stdout --assemble-from '1e' --fasta 2seqs.sammy.fa"#, :log => log
+    end
+    splits = trails.split("\n")
+    splits.length.should == 2
+
+    splits[0].should == ">1e 1e"
+    splits[1][0..60].should == 'TATCCGGTCCCCCTAGAATGTTGATTCCTCCGTCTTCTGATTTCCGTTGGCGGTTCGTATC'
+    splits[1].length.should == 613
+  end
+
+  it 'should work when assembling the entire graph' do
+    data_path = File.join(TEST_DATA_DIR,'explore','1')
+    trails = nil
+    Dir.chdir(data_path) do
+      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} assemble --no-progressbar --quiet --output-pathspec --min-contig-length 0 --output-contigs /dev/stdout --fasta 2seqs.sammy.fa"#, :log => log
+    end
+    splits = trails.split("\n")
+
+    splits[0].should == ">contig1 1s"
+    splits[1][0..60].should == 'AGGGCAGATTCCCACGCGTTACGCACCCGTGCGCCACTAGACCCGAAGGTCTCGTTCGACT'
+    splits[1].length.should == 613
+  end
+
+  it 'should not crash when recoherence kmer is given' do
+    data_path = File.join(TEST_DATA_DIR,'explore','1')
+    trails = nil
+    Dir.chdir(data_path) do
+      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} assemble --no-progressbar --assembly-kmer 7 --recoherence-kmer 51 --quiet --output-pathspec --output-contigs /dev/stdout --fasta 2seqs.sammy.fa"#, :log => log
+    end
+    # Not sure what is supposed to come out of here with such a short assembly-kmer, but just so long as it doesn't crash.
+  end
+
+  it 'should use recoherence' do
+    trails = nil
+    Dir.mktmpdir do |tmpdir|
+      Dir.chdir(tmpdir) do
+        cmd = "#{FINISHM_SCRIPT_PATH} assemble --no-progressbar --assembly-kmer 51 --recoherence-kmer 90 --quiet --output-contigs /dev/stdout --fasta-gz #{TEST_DATA_DIR}/gapfilling/6/reads.random1.fa.gz,#{TEST_DATA_DIR}/gapfilling/6/reads.random2.fa.gz"
+        puts cmd
+        trails = Bio::Commandeer.run cmd
+      end
+    end
+    trails.should == '>contig1
+GTGACGGTGGAGCCCACGCAACGACCCGAGGAGTGGCCGGGTTTACAGCAGCGGGGGGAGCTGGGCAAACCCTCAGTTGACCGGTTCTCACTTATCGGGTCAAAGGATTAGGCATAATAAGGAGAGTTAGAATGTCTTACCTACTTAAAAACGCCCGCAGCAAAGGGACTAACGATGTTTGAACGAGCTCCTGCGCCCATGTGCTGGGTAGGAAGTGCGACCGGGAATTGGTTTTGGATCCAGGCGGATGGGCACTAACCGGCGGTTAAACCACGGGGCTAGTCGCATTGTTACCTAGTGGGTTGAGCGCAACCAATGATGGGCCTCCGCCTCGCGACTCCTCTCGAGTACCTCCTATGTGGGGAGTGATAGGGATTCGGGAATGCCATTTTGACCCTGAGCTGTTGAAGGAACTTTGCAGACGCCCTCACGTATACCTATTAGGGGAACGGTGCTAGGTATTAGATATACTTCTGCCTAGACAATAGCAGCGGTTCTCAGCGCACCACTACCGCACGATAGCCACTCATGGATGCGTTATATCGTGTTCCAAGTCCAAGCGTTCTCCTCGGGTTAGTTCCCATCATAGATGCTGGTGGAGCTCAATCCGGCAGCATAATGAAAGGTTACCCGATGTGGCCTATGTGCGACCTCACTGGAAGGAAACGCAGACGAGGGTAAAAGGCCTCTGGGAGCCCCCCCGCGACTATGCGTGGCCGTGTTTCCTTCCTCTGCATAAGACCCGATCTGTTATTCCTTTAGAGTGCGCCAACCTGGAACTCGCCTCCGCCATCGTGTATCGGAACTAAACTCGCGAGTGTTTGAAACGAACATGATGTAGTTTTCAGGATACTTGATGCATACGCACACGTACTCGCATGCCAAGGTATAGATGCTCCCCGTATGAAGTCACGTGGCCTGATCGCACAGAAACATTTCGGTGGACAGCAGATTCGGAACGACCGCGCAGCGCCGTGAGAAAACGTCACTAAAATAAAAACCATAGGCAAGATATACGAAGCGTGGGTCATTCTACGGCATCAAACGTTTCTATTTGTCTTTCTCGGGCCTGGTACGTTAAAAAACCGGTGGCCACCCCGTATTCCGGTAAAGTCAACTCTGGGACGCAAATGCCGAACACGGTGATTACTCAAAATTTCGTGAGCAGACGCCTACGTTAGTTTGGTAATGAAATATATTTCGGGTCGGTTGTTGGTTTTGGCCACTTCAGATGCATACTGGCCCGACTATCCTATACATTGGAGATTTATCAATGCTTGCATCGGGAGCCCCGATTCGAGCGTATTGTTGGAACAACCATCGCCGCGTCCATAACCACTTGTCAGTTCTTCACATTGCGTTCGGAACGTTCACCCCTCAGGATTTGGGACAGTGTGAATTCGATTGTCTGAAGTGTTTTTAAGCAGGCCTCCAGGTCGCGTGTTTTACATGGGTGGCTCGGGCTGGGACTCCGTGCCGTAGTCGACGTCGACCGCAACTGATGAGCGTATACGGAGATATTACTCTGCGATTTCAAGAGAGCGCCCGGGTTAGGCTGTCGCTTCATAATGACAGTCTGTGCCGGAGAGGGCATGTTAGCCAGGCTAGACCTGCACGGGAACTCTTTAGAGTTAGGAGTAAATATGGAATGCGTAAAATCCTAAGATTGTGACTGTCTAATGACCTCGCGCTGCAAATGCGCATCACTAGTAATAGGGTGGGGATTCGGCAAAACCGATTGATCGTTGCAACGGTTCCCAACTCGAAAGTTCAAAAAATTCAACGAGCAGACTACCGCCATCACCTCCTTTACCTGGGGGAGCTCCCTAGCGGTCCCTAGATTGGGCACAATTGCGCGATGGAGGCCCCGGATGTTCTTGGAAACGCGTTGAACATCATTCATTTAATCTGGAAACTGTTAGACCTGGGCTACTATCCGTTTGTCAGTTCGGAAACTATATTTCATACAGGAATGAATAGGCCCCGATCACCTGCCCCG
+>contig2
+AGCACACCTTGCCCAGATGTGGCCGAAGCCGGGCGCCAGTAGACGGCACCCCTGTATACAGGTCCTCTGCGTCAACCAGGGAACCCCTCCATCGACCGGGGTCGCACACCTTTAATCATAAAAATTGTGTTGTGTAGCGCCTCTCTGGAAAGTAAAGTAACCGCTTTCCCCTGACCACGTGTGACGACCCCCCATTTGGCAAGAGCCCGAGGGACCCGCTGCGTATTATCTCCAACGTCGCAAGTCAGGCGCCTTATTCGGGTGCATCGATATGGCGTCCCCACTTTGAGGTTAGTAGCTTACCAAACCAGAGATACCGTCAAGACTATTCATTTCTCGGACACGTTTCATTTTGGACAGTGATGTGGGTCTGCAAATTCGGGTTTATTTACTTCCCACATGTGGACCTGTGCACTTCTTAGGTTGAAGCCAATGAACAAAGCCTCGTCACCGACGATGCTTACGTTTCTCACCTCGCGTTATTGATTGCCTTGTGCCTTGCGTAATCATAGTCGTCAATCAATGACTTAAGTTATTCCATCCAAATCCCGGGTCACCTCTTATGTAGACAGGAATCCCGCCAACTTTGTACAAAGGGGAACCGGCTAGGGACAATGGCCTCGATAGGAGCCTACCATCTGACTCTTTACAGGACGGTTGGCACGAACAGATGCGAATTTCTAATACCATGTTAATAGCCCTCTGGGGATCGCGCCGGCTACGTAATGGTCGCGGCTGGATGTTCCGGCTTAAAAGTTTGGCAACCTGTGGACTCAACGTCGCTTGTCAATCGGATCCCGGAAGCCCTATAACCTTTTGTCAGCTCTGAACTAACAGGCATGGTGGAGCTAAGCACTCATTAGCTTGCAATTATTACAGGATGATATGCCACAAGATCTACGAGTGATTTGAAGGCACACTCCCCGAGGTGGTACCGATGAAATAGGTGGTGCTATCGAAATATATTTCATTACCAAACTAACGTAGGCGTCTGCTCACGAAATTTTGAGTAATCACCGTGTTCGTGAGACCTTAAGGTCCGGGGCTACCAGAGCCGATGGATCGGAGCGCCCGAACAACGTGAAGGTGACTACGTTCTACCACGGTTGACTCGTACGTCGACTAGCAAATTCTTGGACTTTAGGGGCGAAAAAAGTTGGAATAATTCTTCTCGGCTTGGGTGATAGCTTTCCACCTAACCCTAAGGAGTGTAGTGCAATAGTGGATGTTATTCAGGTTGCAACTCTAGTTGGGCCCGGAACCATGCCGTAGAATGACCCACGCTTCGTATATCTTGCCTATGGTTTTTATTTTAGTGACGTTTTCTCGCTTTTACCCGGCTCGAAAAGCGTGGGGCCCGTTTAGACCGCGGGCGTCCGCTGGCCTATTGATCAGAGTTGTCTAGCGCGTCGAGGAGGGTGGCATGATTTACAGCTTCCGCCTGAGCAACGGACGGATGTGTCCGGGGTGTAACCCATCTATAAGCTATCGTCAGAGTTGTGATCCTAGTAGCTATTATAGCAAGGCTGTAGGGATCGTCGCGGGGACTGACCAATACGCACCCGTTCCCGAGGACGGGAATCCACCAGAGTTTGGGTCTTCTTTCGCCATTGGTTGCTACTGCCAACACTTCTGACCTGCGGGAGTCAGTAGGACCCCAGACTTAATAATCCGCCCACGGCGAAGGAGTATTCGTACACAATCAGAGGCGGCAGAGCGCTAGCGGGGCAGCGTCAGCGCCTGCGGCGCATTGAGTTGGCTGGCGACCAGAGGTTAAGCTTCGATGGTCGGCCCCTTGCAAGGCCCTTTAACAGTTTTAGGACACGCGTGCCTCAGCATTAGTAGTGTCACCTCCCGTCCACGTCCACCTTAGTGTTTTGCGCGCTGCCACGTAGTACTGCGCTTAGCTTCTTCTGGTGGAAACGGACCTGGATTACTAACAAAGATGGTGTAGCAAGACCCGCCAGGTCAATTCAATTTCGGCCGCATTCCACCGACGATTAGTTTGAAAGGGTTATAGGAGCCGAGATCTGCTCGGGGGGACTTACAGTCTACTTCATGATCCGTACGCAGCGGTAGGTATGGCGTTACAGAGTTGAATGAATTCTCAGCACCGATGAACGATG
+'
+  end
+
+  it 'should output contig stats' do
+    data_path = File.join(TEST_DATA_DIR,'explore','1')
+    stats = nil
+    Dir.chdir(data_path) do
+      stats = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} assemble --no-progressbar --min-contig-length 0 --quiet --output-pathspec --output-contigs /dev/null --output-contig-stats /dev/stdout --fasta 2seqs.sammy.fa"#, :log => log
+    end
+    #        +contig1 21.15370018975332
+    #        +contig2 62.07488986784141
+    #        +contig3 22.654135338345863
+    #        +contig4 34.90963855421687
+    # ...
+    puts stats
+    stats.match(/name\tcoverage\ncontig1\t21.15370018975332\ncontig2\t62.07488986784141\ncontig3\t22.654135338345863\n/).nil?.should == false
+  end
+
+  it 'should bubbly assemble' do
+    trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} assemble --bubbly --no-progressbar --quiet --output-contigs /dev/stdout --fasta-gz "+
+      "#{TEST_DATA_DIR}/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz"
+    #  --output-pathspec
+    answer = <<EOF
+>contig1
+GACCCGCGTGAGCTCTTAAGTACCTAGACTTCACTCCCGGCTTTAGAGTAGTATCGGTACGGGACTCCCTGACCTAAGTT
+AGGACGGCGTCCGCCGTAGAACGTGGATGATCTGAAGCATTTCGGAGCAGGCCCTAAGCGCGGCTCCTCTTCCATCGCAG
+TCCAAACGCCATTTCAGTTAGTGCGCGCGAGCAGCTCCAGGAGAGCGCTCCGGTGAAACTATCCGTTTGTATACGTCTCC
+TACCTGATTCCAGACCAACAAACGGTAACCCTAGCTAAGACTCGTTGCTGAGACCACATCAATCAAGGCGACAGGGAATA
+GGAAGTTAGTCTCGAAATTAGCTACAGGGACGTACACCTATTACCGAGCCCACTCGCTAACTCTAACTAAGACTCCTGCG
+CCACCGGCAAACATGTTGAACTTCTTATTTCGGCCGTCCAATTAAATCGTTCTTGGTGTGGCGACTACATTAAACATTAT
+CACATGCCGGCATTTGTTCAACTTCTAGGGGCCCCGGAATTGGCCTGACCCTCTTAAGGCTGTTGCCGTACGATTGAATC
+AGTAGTTGGTTGACGATAGCCCCCGGGGTACAGAGGCTCCTAGTCGCATTTATTTGAGTAACGCAGGCCCATGAAAGATG
+GCCTTCGACAAAAAGTAATTAAGCACCGTATAATTTGTGGGTGATTTGCCGGAACATAACATTCCTACCTGACCGAGTCT
+CTATTAACCAGCGGGCAGGTGACGAAATGCGCCACACTACTCCTCTGACAGCTGAGGATCACAGCCGAGATGTAAGTCTC
+AGCAATAGGCAAAACCCGAATAGTTTTTGGGATATAGGAACTCCTTGCCTCTACCGTTTGCGCGCAGATGCCATAAGGTG
+CACGCCATCTAACCGTCCTCGCCGTATCGTGTCTCTGGCGAGCTTTTAATGGCAACATAGAACTTACATTTATAACGCGC
+ATAGGACCCATCATACCTGCCACTTTTGAAGGGGATCCACGTTTCCTAAATCAGAATACTGATTAATTAATTTACGGATG
+TATACCCACAGTCTGTAGAAATAGAAAAGGTTGTAACGTGCATCCCGGCGACACTGGTAATGGTGCGTCTTGCTTCGGAG
+GTTGATTTATTGTGCCCCCCGTCACACAGCATCCCTCCGACGTGTTAAGTTAGTAAGCAACATTAAAAAAAACTCACGCT
+CGATCTTACGTATCTTCGAAGGACGGTATGGGATGGTAGGTCGCCTGCGGGGTACTGTGGCAACGCACGGATCTTAATAC
+GGAGCTATCGCGTGTATACCGTACGGGAGAACTGCGGATTAGCTATAGCAAAAAACTACGGTGTCCCATTCGCCGTAAAG
+TAACGCAGTAGGGAGGGGGGGCCGATCATGGTCCACAACCTAGGGCATGCCTCCTCGGTAAAACACTATCCCCAGAGTTG
+TAAACTAGCCTGGGAGCAGGTACTTGAAGCACCTTGCATCTTTAACTTAGCTTACGATGGAGACTACCCACCCGATAATG
+ACTGCTTTGGCGTGGACCTCTGGATGAAGAACGGACTTCCTTACCAGCGCGGAATTGTGGTTCATCTGGACCCAGTTCCG
+ACCTGAGCATTCGGTTCGGCTAACGAATGTAAATCGGTCTGAAACAGTGATCCTCGCTGCCTATACGTTGACAGTGGTCA
+AATACAACGTTAGTGGTTCTTTCTTACATCATTATCGTGCTAGCCCTGCGCTTCTCTTCCCAAATGGCTTCTAATCCTGT
+ACCTGGAATCATTCTCTCAGCCCGGATCGAGTTCTGCCGGGATAACGCCGATTACGCATACTTACGTAAAAGACCAGAGG
+ATTAGCACTGCGATAAGGCCGTAATGAAGGTAAGAGGGAAACAGATCATTTGGGTATATATCACAACTGTCGCCCCCTTT
+AGCTGTGTAGTCATATGTCGCCAGTACGAAATATTATCCCAATGCAGTGTCCGGCCTTCGCATTTGTCACGGCATGCTTG
+AAAGATAGCGGTGGGGTTGAGCAGCGTGGGCGCTCCTTCAGATCACCGCACTGTATGGCAGCTCGCTCCGGTAATAGTCT
+GCACGAACCGACGCAACATCAGTATCGGGTACGATAGTTAAGAGATACGTGCAGTAGCATGCTCTCTTTGGCAGAGCGCC
+CCCTCGAGCAATTTATGGCCCAAGACTCAACAGACAAGCATCGTGTGGCGATGAGTAACTATGCCAGACGAGTTGACTGG
+TAGTTGTGACGCTCATTGTCTCAATCAATCGGTGGTCGTCACGGGACCAGACTGCCCCCATTTGGCTCGCTGTGAACCCG
+AGACGTAATGTCAGGACTCTCTGGGGTCGTGGGAATCATCCAAGTACCCAACCCCCCGGAGTCATGGGCGCAACATCCGT
+CTCAGAATGATTTTGAAGGAAGCTCTGGGAAGGTTCAATTAATGAACTGGTCGGCATAATTATTCATTCGTATCGGCTCG
+ATCTGAGAGATGGATATGGAAAAATCAAGATAACGCCCATTTGACCGACCGTACCTTAAAGCAGACGCGAATTATAGCGA
+GCGGTTATACCAGCAATAATTATGGGGGTAGACTTGTTCGTGTAGACAGCGTAATAATTCCGTCAGGTGCACTTTGCTGT
+CTTAACCGGCCGGTAGTCGAGCGGACAGGTCCACCGCACTAGGTGGTGCTATTCGATGGTTTCATGCCACCACGCAAGGC
+TAACACGGTCGCGCATATACATCCCGACAGACAAGAGTGGATGCTTCATTGATTGCTTGATAATCTCTTGTACAGGAGAT
+TGTTGGCGTGTCATACCGATAAGATGCTGCCATACATAGGCAGACTGGGCCGGATTCTACAGTCGGTGGGCTGCAGCCGA
+AGCTTAGTTGTGCAGGTCGTAGCGATAAGCGAGTCTTGTTTACGGTTAACCCCCGTCTCCTGCAACTATAACCGAGGGAA
+TCGTGACTACCAAGAGCCCTATGAGATCCCTC
+EOF
+    answer = answer.gsub(/([ATGC])\n/,'\1')+"\n"
+    trails.should == answer
+  end
+
+  it 'bubbly assembler should output pathspec' do
+    command = "#{FINISHM_SCRIPT_PATH} assemble --output-pathspec --bubbly --no-progressbar --quiet --output-contigs /dev/stdout --fasta-gz "+
+      "#{TEST_DATA_DIR}/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz"
+    puts command
+    trails = Bio::Commandeer.run command
+    answer = <<EOF
+>contig1 1s,2s,3s
+GACCCGCGTGAGCTCTTAAGTACCTAGACTTCACTCCCGGCTTTAGAGTAGTATCGGTACGGGACTCCCTGACCTAAGTT
+AGGACGGCGTCCGCCGTAGAACGTGGATGATCTGAAGCATTTCGGAGCAGGCCCTAAGCGCGGCTCCTCTTCCATCGCAG
+TCCAAACGCCATTTCAGTTAGTGCGCGCGAGCAGCTCCAGGAGAGCGCTCCGGTGAAACTATCCGTTTGTATACGTCTCC
+TACCTGATTCCAGACCAACAAACGGTAACCCTAGCTAAGACTCGTTGCTGAGACCACATCAATCAAGGCGACAGGGAATA
+GGAAGTTAGTCTCGAAATTAGCTACAGGGACGTACACCTATTACCGAGCCCACTCGCTAACTCTAACTAAGACTCCTGCG
+CCACCGGCAAACATGTTGAACTTCTTATTTCGGCCGTCCAATTAAATCGTTCTTGGTGTGGCGACTACATTAAACATTAT
+CACATGCCGGCATTTGTTCAACTTCTAGGGGCCCCGGAATTGGCCTGACCCTCTTAAGGCTGTTGCCGTACGATTGAATC
+AGTAGTTGGTTGACGATAGCCCCCGGGGTACAGAGGCTCCTAGTCGCATTTATTTGAGTAACGCAGGCCCATGAAAGATG
+GCCTTCGACAAAAAGTAATTAAGCACCGTATAATTTGTGGGTGATTTGCCGGAACATAACATTCCTACCTGACCGAGTCT
+CTATTAACCAGCGGGCAGGTGACGAAATGCGCCACACTACTCCTCTGACAGCTGAGGATCACAGCCGAGATGTAAGTCTC
+AGCAATAGGCAAAACCCGAATAGTTTTTGGGATATAGGAACTCCTTGCCTCTACCGTTTGCGCGCAGATGCCATAAGGTG
+CACGCCATCTAACCGTCCTCGCCGTATCGTGTCTCTGGCGAGCTTTTAATGGCAACATAGAACTTACATTTATAACGCGC
+ATAGGACCCATCATACCTGCCACTTTTGAAGGGGATCCACGTTTCCTAAATCAGAATACTGATTAATTAATTTACGGATG
+TATACCCACAGTCTGTAGAAATAGAAAAGGTTGTAACGTGCATCCCGGCGACACTGGTAATGGTGCGTCTTGCTTCGGAG
+GTTGATTTATTGTGCCCCCCGTCACACAGCATCCCTCCGACGTGTTAAGTTAGTAAGCAACATTAAAAAAAACTCACGCT
+CGATCTTACGTATCTTCGAAGGACGGTATGGGATGGTAGGTCGCCTGCGGGGTACTGTGGCAACGCACGGATCTTAATAC
+GGAGCTATCGCGTGTATACCGTACGGGAGAACTGCGGATTAGCTATAGCAAAAAACTACGGTGTCCCATTCGCCGTAAAG
+TAACGCAGTAGGGAGGGGGGGCCGATCATGGTCCACAACCTAGGGCATGCCTCCTCGGTAAAACACTATCCCCAGAGTTG
+TAAACTAGCCTGGGAGCAGGTACTTGAAGCACCTTGCATCTTTAACTTAGCTTACGATGGAGACTACCCACCCGATAATG
+ACTGCTTTGGCGTGGACCTCTGGATGAAGAACGGACTTCCTTACCAGCGCGGAATTGTGGTTCATCTGGACCCAGTTCCG
+ACCTGAGCATTCGGTTCGGCTAACGAATGTAAATCGGTCTGAAACAGTGATCCTCGCTGCCTATACGTTGACAGTGGTCA
+AATACAACGTTAGTGGTTCTTTCTTACATCATTATCGTGCTAGCCCTGCGCTTCTCTTCCCAAATGGCTTCTAATCCTGT
+ACCTGGAATCATTCTCTCAGCCCGGATCGAGTTCTGCCGGGATAACGCCGATTACGCATACTTACGTAAAAGACCAGAGG
+ATTAGCACTGCGATAAGGCCGTAATGAAGGTAAGAGGGAAACAGATCATTTGGGTATATATCACAACTGTCGCCCCCTTT
+AGCTGTGTAGTCATATGTCGCCAGTACGAAATATTATCCCAATGCAGTGTCCGGCCTTCGCATTTGTCACGGCATGCTTG
+AAAGATAGCGGTGGGGTTGAGCAGCGTGGGCGCTCCTTCAGATCACCGCACTGTATGGCAGCTCGCTCCGGTAATAGTCT
+GCACGAACCGACGCAACATCAGTATCGGGTACGATAGTTAAGAGATACGTGCAGTAGCATGCTCTCTTTGGCAGAGCGCC
+CCCTCGAGCAATTTATGGCCCAAGACTCAACAGACAAGCATCGTGTGGCGATGAGTAACTATGCCAGACGAGTTGACTGG
+TAGTTGTGACGCTCATTGTCTCAATCAATCGGTGGTCGTCACGGGACCAGACTGCCCCCATTTGGCTCGCTGTGAACCCG
+AGACGTAATGTCAGGACTCTCTGGGGTCGTGGGAATCATCCAAGTACCCAACCCCCCGGAGTCATGGGCGCAACATCCGT
+CTCAGAATGATTTTGAAGGAAGCTCTGGGAAGGTTCAATTAATGAACTGGTCGGCATAATTATTCATTCGTATCGGCTCG
+ATCTGAGAGATGGATATGGAAAAATCAAGATAACGCCCATTTGACCGACCGTACCTTAAAGCAGACGCGAATTATAGCGA
+GCGGTTATACCAGCAATAATTATGGGGGTAGACTTGTTCGTGTAGACAGCGTAATAATTCCGTCAGGTGCACTTTGCTGT
+CTTAACCGGCCGGTAGTCGAGCGGACAGGTCCACCGCACTAGGTGGTGCTATTCGATGGTTTCATGCCACCACGCAAGGC
+TAACACGGTCGCGCATATACATCCCGACAGACAAGAGTGGATGCTTCATTGATTGCTTGATAATCTCTTGTACAGGAGAT
+TGTTGGCGTGTCATACCGATAAGATGCTGCCATACATAGGCAGACTGGGCCGGATTCTACAGTCGGTGGGCTGCAGCCGA
+AGCTTAGTTGTGCAGGTCGTAGCGATAAGCGAGTCTTGTTTACGGTTAACCCCCGTCTCCTGCAACTATAACCGAGGGAA
+TCGTGACTACCAAGAGCCCTATGAGATCCCTC
+EOF
+    answer = answer.gsub(/([ATGC])\n/,'\1')+"\n"
+    trails.should == answer
+  end
+end