finishm 0.0.1

data/spec/kmer_coverage_based_path_filter_spec.rb

@@ -0,0 +1,73 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio'
+
+class DummyTrail
+  attr_accessor :sequence
+
+  def initialize(seq)
+    @sequence = seq
+  end
+
+  def self.trails(seqs)
+    seqs.collect{|s| DummyTrail.new(s)}
+  end
+end
+
+#Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')
+
+describe "kmer coverage path filter" do
+  it 'should rule things out when no appropriate kmers are present' do
+    kmers = Bio::KmerMultipleAbundanceHash.new
+    kmers['AAAA'] = [0, 0]
+    trail = DummyTrail.new('ATATATTTA')
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter([trail], kmers, [1]*2)
+    paths.should == []
+  end
+
+  it 'should not rule things out when appropriate kmers are present' do
+    kmers = Bio::KmerMultipleAbundanceHash.new
+    kmers['ATATATTT'] = [1, 10]
+    kmers['TATATTTA'] = [3, 1]
+    trail = DummyTrail.new('ATATATTTA')
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter([trail], kmers, [1]*2)
+    paths.collect{|t| t.sequence}.should == %w(ATATATTTA)
+  end
+
+  it 'should not accept different thresholds for different timepoints' do
+    kmers = Bio::KmerMultipleAbundanceHash.new
+    kmers['ATATATTT'] = [1, 10]
+    kmers['TATATTTA'] = [1, 3]
+    trail = DummyTrail.new('ATATATTTA')
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter([trail], kmers, [2]*2)
+    paths.should == []
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter([trail], kmers, [0,2])
+    paths.collect{|t| t.sequence}.should == %w(ATATATTTA)
+  end
+
+  it 'should rule some things out in a figure 8 style graph' do
+    kmers = Bio::KmerMultipleAbundanceHash.new
+    kmers['ATA'] = [1, 10]
+    kmers['AGA'] = [1, 10]
+    kmers['TAG'] = [1, 10]
+    kmers['GAT'] = [1, 10]
+    kmers['ATC'] = [1, 10]
+    kmers['AGC'] = [1, 10]
+    trails = DummyTrail.trails %w(ATATC ATAGC AGATC AGAGC)
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter(trails, kmers, [1]*2)
+    paths.collect{|t| t.sequence}.should == %w(ATAGC AGATC)
+  end
+
+  it 'should respect exclusion of filtering at the ends' do
+    kmers = Bio::KmerMultipleAbundanceHash.new
+    kmers['ATATATTT'] = [1, 10]
+    kmers['TATATTTA'] = [3, 1]
+    trail = DummyTrail.new('GATATATTTAC')
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter([trail], kmers, [1]*2)
+    paths.collect{|t| t.sequence}.should == %w()
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter([trail], kmers, [1]*2, :exclude_ending_length => 1)
+    paths.collect{|t| t.sequence}.should == %w(GATATATTTAC)
+    trail = DummyTrail.new('GATATATTTAGC')
+    paths = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new.filter([trail], kmers, [1]*2, :exclude_ending_length => 1)
+    paths.collect{|t| t.sequence}.should == %w()
+  end
+end

data/spec/kmer_profile_finder_spec.rb

@@ -0,0 +1,38 @@
+require 'rspec'
+require 'pp'
+require 'systemu'
+
+# To run this test:
+# $ rspec /path/to/test_script_being_tested.rb
+
+# Assumes that the name of the file being tested is ../something.rb relative to the directory containing this test scripts, and the name of this tes script is test_something.rb
+$:.unshift File.join(File.dirname(__FILE__),'..')
+script_under_test = File.basename(__FILE__).gsub(/_spec.rb$/,'.rb')
+path_to_script = File.join(File.dirname(__FILE__),'..','bin',script_under_test)
+
+
+describe script_under_test do
+  it 'should scripting test ok' do
+inputs = <<EOF
+AAAAAAAAAATCAACCAAAATGTTCCATCACTTGACAATTTTTGGTTATCGGTTGTATACCTCAAGATTTGCTACTTTGTCAGAAGAGGGGAAAAAAAAGC 36 0 0 18 29 37 32 0 0 41
+AAAAAAAAAGACGCCCGTTCACCGGGCGCCTCTTGTTGTGAAATGAATTATCTCCGATGGTTCGTTATCTGATCGCCTCTTCGGTCTCGGCATCGAAGATG 0 0 0 0 0 0 0 0 0 0
+AAAAAAAAAGATCTCAGCCTCTAAGAAACGAAAACATGGTCTCTCTCAATCCATAACGTCGCCTGTTGATCGCGTTCTGTTACTTCAAAGAACCTTCGGCA 0 0 0 0 0 0 0 0 0 0
+AAAAAAAAATCAACCAAAATGTTCCATCACTTGACAATTTTTGGTTATCGGTTGTATACCTCAAGATTTGCTACTTTGTCAGAAGAGGGGAAAAAAAAGCC 2121 0 0 1416 1790 2229 2115 0 1 2399
+AAAAAAAAATCAACCAAAATGTTCCATCACTTGACAATTTTTGGTTATCGGTTGTATACCTCAAGATTTGCTACTTTGTCAGAAGAGGGGAAAAAAAGCCA 68 0 0 49 60 94 80 0 0 86
+AAAAAAAACAATAGGTTTGTACTCCCGTTAGAGGTGCTGCCACCACGGTGGTTGCTGAGAACACACTCTTGGAACCTGATTCGGATAATGCCGACGAAGGA 0 0 0 0 0 0 0 0 0 0
+AAAAAAAACCCAGCAACGGTTACATACGCTCAGAGCAGAAGAAAAAAAAGCATCGCGCTCACTAACGGGTCTTCAACGGCAGCGTCACTCCATCACGCTGT 0 0 0 0 0 0 0 0 0 0
+AAAAAAAACCCGAATCAGATGCTGGTACTCAAGGTCTTAAAGACCGTTGTCCTATCAGCAGATAAAAAATCCCATATCAAGCAGAGGATAGAGCACCTCAA 2 0 0 0 0 0 0 0 0 1
+AAAAAAAAGACGCCCGTTCACCGGGCGCCTCTTGTTGTGAAATGAATTATCTCCGATGGTTCGTTATCTGATCGCCTCTTCGGTCTCGGCATCGAAGATGT 0 0 0 0 0 0 0 0 0 0
+AAAAAAAAGAGAATAGTGATCAAGTTTGATAGTACATCGACGTTTTAGCTGATAGCTTCCTCCAGAAGCTGTCTGCCATAAACCTGCGCATATTCACCGTT 0 0 0 0 0 0 0 0 0 0
+EOF
+
+    status, stdout, stderr = systemu "#{path_to_script} --threshold 1000 -", 'stdin' => inputs
+    raise stderr if stderr != ''
+    stderr.should eq("")
+    status.exitstatus.should eq(0), "testing #{path_to_script}"
+
+    expected = (1..632).collect{|s| "#{s}\t"}.join("\n")+
+      "\n633\t1\n"
+    stdout.should eq(expected)
+  end
+end

data/spec/kmers_count_tabulate_spec.rb

@@ -0,0 +1,120 @@
+require 'rspec'
+require 'pp'
+require 'systemu'
+require 'tempfile'
+
+# To run this test:
+# $ rspec /path/to/test_script_being_tested.rb
+
+# Assumes that the name of the file being tested is ../something.rb, and the name of this script is test_something.rb
+$:.unshift File.join(File.dirname(__FILE__),'..')
+script_under_test = File.basename(__FILE__).gsub(/_spec/,'')
+def assert_equal(e,o); o.should eq(e); end
+path_to_script = File.join(File.dirname(__FILE__),'..','bin',script_under_test)
+
+
+
+describe script_under_test do
+  it 'should single file test' do
+    Tempfile.open('spec') do |temp1|
+      temp1.puts 'AAA 1'
+      temp1.puts 'AAT 2'
+      temp1.close
+
+      status, stdout, stderr = systemu "#{path_to_script} #{temp1.path}"
+      stderr.should eq("")
+      status.exitstatus.should eq(0)
+      stdout.should eq(["\t#{File.basename temp1.path}",
+      "AAA\t1",
+      "AAT\t2"].join("\n")+"\n")
+    end
+  end
+
+  it 'should two file test' do
+    Tempfile.open('spec') do |temp1|
+      temp1.puts 'AAA 1'
+      temp1.puts 'AAT 2'
+      temp1.close
+
+      Tempfile.open('spec') do |temp2|
+        temp2.puts 'AAA 1'
+        temp2.puts 'ATA 3'
+        temp2.close
+
+        status, stdout, stderr = systemu "#{path_to_script} #{temp1.path} #{temp2.path}"
+        stderr.should eq("")
+        status.exitstatus.should eq(0)
+        stdout.should eq(["\t#{File.basename temp1.path}\t#{File.basename temp2.path}",
+        "AAA\t1\t1",
+        "AAT\t2\t0",
+        "ATA\t0\t3"].join("\n")+"\n")
+      end
+    end
+  end
+
+
+  it 'should two file test as percentage' do
+    Tempfile.open('spec') do |temp1|
+      temp1.puts 'AAA 1'
+      temp1.puts 'AAT 3'
+      temp1.close
+
+      Tempfile.open('spec') do |temp2|
+        temp2.puts 'AAA 1'
+        temp2.puts 'ATA 4'
+        temp2.close
+
+        status, stdout, stderr = systemu "#{path_to_script} --percentage --trace error #{temp1.path} #{temp2.path}"
+        stderr.should eq("")
+        status.exitstatus.should eq(0)
+        stdout.should eq(["\t#{File.basename temp1.path}\t#{File.basename temp2.path}",
+        "AAA\t0.25\t0.2",
+        "AAT\t0.75\t0",
+        "ATA\t0\t0.8"].join("\n")+"\n")
+      end
+    end
+  end
+
+  it 'should cutoff kmers with overly low abundances' do
+    Tempfile.open('spec') do |temp1|
+      temp1.puts 'AAA 1'
+      temp1.puts 'AAT 2'
+      temp1.close
+
+      Tempfile.open('spec') do |temp2|
+        temp2.puts 'AAT 1'
+        temp2.puts 'ATA 3'
+        temp2.close
+
+        status, stdout, stderr = systemu "#{path_to_script} --trace error --min-count 2 #{temp1.path} #{temp2.path}"
+        raise stderr unless stderr.nil? or stderr==''
+        status.exitstatus.should eq(0)
+        stdout.should eq(["\t#{File.basename temp1.path}\t#{File.basename temp2.path}",
+        "AAT\t2\t1",
+        "ATA\t0\t3"].join("\n")+"\n")
+      end
+    end
+  end
+
+  it 'should two file test as percentage with min count' do
+    Tempfile.open('spec') do |temp1|
+      temp1.puts 'AAA 1'
+      temp1.puts 'AAT 3'
+      temp1.close
+
+      Tempfile.open('spec') do |temp2|
+        temp2.puts 'AAT 1'
+        temp2.puts 'ATA 4'
+        temp2.close
+
+        status, stdout, stderr = systemu "#{path_to_script} --percentage --min-count 2 --trace error #{temp1.path} #{temp2.path}"
+        stderr.should eq("")
+        status.exitstatus.should eq(0)
+        stdout.should eq(["\t#{File.basename temp1.path}\t#{File.basename temp2.path}",
+        "AAT\t0.75\t0.2",
+        "ATA\t0\t0.8"].join("\n")+"\n")
+      end
+    end
+  end
+end
+

data/spec/oriented_node_trail_spec.rb

@@ -0,0 +1,221 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio'
+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 String
+  def revcom
+    Bio::Sequence::NA.new(self).reverse_complement.to_s.upcase
+  end
+end
+
+describe "OrientedNodeTrail" do
+  it "should be able to store a sequence of oriented nodes" do
+    graph = Bio::Velvet::Graph.parse_from_file File.expand_path("#{TEST_DATA_DIR}/velvet_test_trails/Assem/LastGraph")
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+
+    trail.to_a.length.should == 0
+    trail.add_node graph.nodes[1], :start_is_first
+    trail.to_a.length.should == 1
+    trail.to_a[0].node.should == graph.nodes[1]
+    trail.to_a[0].first_side.should == :start_is_first
+
+    trail.add_node graph.nodes[2], :start_is_first
+    trail.add_node graph.nodes[4], :end_is_first
+    trail.to_a.length.should == 3
+    trail.to_a[2].node.should == graph.nodes[4]
+    trail.to_a[2].first_side.should == :end_is_first
+
+    expect {trail.add_node graph.nodes[4], :no_side}.to raise_error
+  end
+
+  it 'should get the sequence of no nodes' do
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    trail.sequence.should == ''
+  end
+
+  it 'should get the sequence of one node' do
+    graph = Bio::Velvet::Graph.parse_from_file File.expand_path("#{TEST_DATA_DIR}/velvet_test_trails/Assem/LastGraph")
+
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    trail.add_node graph.nodes[1], :start_is_first
+    trail.sequence.should == graph.nodes[1].sequence
+    trail.sequence
+
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    trail.add_node graph.nodes[1], :end_is_first
+    trail.sequence.should == graph.nodes[1].sequence.revcom
+  end
+
+
+  it 'should get the sequence of three nodes' do
+    graph = Bio::Velvet::Graph.parse_from_file File.expand_path("#{TEST_DATA_DIR}/velvet_test_trails/Assem/LastGraph")
+
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    trail.add_node graph.nodes[1], :start_is_first
+    trail.add_node graph.nodes[2], :start_is_first
+    trail.add_node graph.nodes[4], :end_is_first
+    exp = 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
+CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
+ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
+GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
+ACTATGCTGGTATTTCACTTCCAGGTACAGG'.gsub(/\n/,'')
+    trail.sequence.should == exp
+  end
+
+  it 'should not do sequence right when there is not enough info' do
+    graph = Bio::Velvet::Graph.parse_from_file File.expand_path("#{TEST_DATA_DIR}/velvet_test_trails/Assem/LastGraph")
+
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    trail.add_node graph.nodes[2], :start_is_first
+    expect {trail.sequence}.to raise_error
+  end
+
+#  # Below are two things I was testing, which I think might be a problem with velvet, but not sure.
+#  it 'should not have the bug I found any more full' do
+#    # This graph is somewhat abbreviated and not a full and complete LastGraph file, but should be ok
+#    lastgraph = <<EOF
+#5     2805    43      1
+#NODE    1      71      0       0       13651   13188
+#ATAGATTATTTTTATTTTTCAGAGAATTTACAGAAAGATCAGTTAAAATCCAGAGCAAGAAAAGCATTGCA
+#AAATTCTCTGAAAAATAAAAATAATCTATGCTGCTCGGTTTGACAAATTTTATCCCGTAAACTCCCTTTTT
+#NODE    2      47      0       0       9848    9462
+#GAAATTAAAAGAAGCTAAAGAGATTCAAAAATCGATCGATAACAAGA
+#ATTTCTGCAATGCTTTTCTTGCTCTGGATTTTAACTGATCTTTCTGT
+#NODE    3      11      0       0       2338    2246
+#AACAGCTTCCA
+#AGCTTCTTTTA
+#NODE    4     2       0       0       396     378
+#TA
+#CA
+#NODE    5     36      0       0       7023    6808
+#TCATCAACAAGCTCAGCTTTGGATTTATCGAATTCT
+#AGGAGTTTACGGGATAAAATTTGTCAAACCGAGCAG
+#ARC     1      2      202
+#EOF
+#    lastgraph.gsub!(/ +/,"\t")
+#    Tempfile.open('spec') do |f|
+#      f.puts lastgraph
+#      f.close
+#
+#      graph = Bio::Velvet::Graph.parse_from_file f.path
+#      graph.nodes.length.should == 5
+#      trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+#      trail.add_node graph.nodes[3], :end_is_first
+#      trail.add_node graph.nodes[2], :end_is_first
+#      trail.add_node graph.nodes[1], :end_is_first
+#      trail.add_node graph.nodes[4], :start_is_first
+#      trail.add_node graph.nodes[5], :start_is_first
+#      trail.sequence.should == 'TGGAAGCTGTTTCTTGTTATCGATCGATTTTTGAATCTCTTTAGCTTCTTTTAATTTCTGCAATGCTTTTCTTGCTCTGGATTTTAACTGATCTTTCTGTAAATTCTCTGAAAAATAAAAATAATCTAT GCTGCTCGGTTTGACAAATTTTATCCCGTAAACTCCTTTTTTATCATCAACAAGCTCAGCTTTGGATTTATCGAATTCT'
+#    end
+#  end
+#
+#  it 'should not have the bug I found any more cut down version' do
+#    # This graph is somewhat abbreviated and not a full and complete LastGraph file, but should be ok
+#    lastgraph = <<EOF
+#416     2705    43      1
+#NODE    62      71      13651   13188   0       0
+#ATAGATTATTTTTATTTTTCAGAGAATTTACAGAAAGATCAGTTAAAATCCAGAGCAAGAAAAGCATTGCA
+#AAATTCTCTGAAAAATAAAAATAATCTATGCTGCTCGGTTTGACAAATTTTATCCCGTAAACTCCCTTTTT
+#NODE    165     2       396     378     0       0
+#TA
+#CA
+#ARC	-62	165	198
+#EOF
+#    lastgraph.gsub!(/ +/,"\t")
+#    Tempfile.open('spec') do |f|
+#      f.puts lastgraph
+#      f.close
+#
+#      graph = Bio::Velvet::Graph.parse_from_file f.path
+#      graph.nodes.length.should == 2
+#      trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+#      trail.add_node graph.nodes[62], :end_is_first
+#      trail.add_node graph.nodes[165], :start_is_first
+#      trail.sequence.should == 'TGCAATGCTTTTCTTGCTCTGGATTTTAACTGATCTTTCTGTAAATTCTCTGAAAAATAAAAATAATCTAT GCTGCTCGGTTTGACAAATTTTATCCCGTAAACTCCTTTTTTA'
+#    end
+#  end
+
+  it 'should give only 1 direction when entering a 2 node loop' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,4],
+      [4,2],
+    ])
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    trail.add_node graph.nodes[1], :start_is_first
+    trail.add_node graph.nodes[2], :start_is_first
+    trail.neighbours_of_last_node(graph).collect{|n| [n.node.node_id, n.first_side]}.should == [[4,:start_is_first]]
+  end
+
+  it 'should to_shorthand' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,4],
+      [4,2],
+    ])
+    trail = Bio::Velvet::Graph::OrientedNodeTrail.new
+    trail.to_shorthand.should == ''
+    trail.add_node graph.nodes[1], :start_is_first
+    trail.to_shorthand.should == '1s'
+    trail.add_node graph.nodes[2], :end_is_first
+    trail.to_shorthand.should == '1s,2e'
+  end
+
+  it 'should be able to parse super-shorthand form easy' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,3],
+      [2,4],
+      [4,2],
+    ])
+    Bio::Velvet::Graph::OrientedNodeTrail.create_from_super_shorthand('2,3', graph).to_shorthand.should == '2s,3s'
+    Bio::Velvet::Graph::OrientedNodeTrail.create_from_super_shorthand('1,2,3', graph).to_shorthand.should == '1s,2s,3s'
+    Bio::Velvet::Graph::OrientedNodeTrail.create_from_super_shorthand('3,2,1', graph).to_shorthand.should == '3e,2e,1e'
+
+    expect {
+      #one node only not enough
+      Bio::Velvet::Graph::OrientedNodeTrail.create_from_super_shorthand('3', graph).to_shorthand
+    }.to raise_error
+    expect {
+      # 2,4 have confusing connections
+      Bio::Velvet::Graph::OrientedNodeTrail.create_from_super_shorthand('2,4', graph).to_shorthand
+    }.to raise_error
+    expect {
+      # 1,4 not directly connected
+      Bio::Velvet::Graph::OrientedNodeTrail.create_from_super_shorthand('1,4', graph).to_shorthand
+    }.to raise_error
+
+  end
+
+  it 'should calculate coverage' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,3],
+    ])
+    path = Bio::Velvet::Graph::OrientedNodeTrail.create_from_super_shorthand('1,2,3', graph)
+    path.coverage.should == 0.5
+    graph.nodes[2].coverages = [10]
+    (path.coverage*100).round.should == (20.0 / 3 / 10 *100).round
+  end
+
+  it 'should give the right neighbours when neighbours are the s and e of the same node' do
+    graph, initial_path, terminal  = GraphTesting.emit_ss([
+      [1,2],
+    ],1,1)
+    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 = false
+    graph.arcs.push arc
+    graph.neighbours_of(graph.nodes[1], :start_is_first).collect{|n| n.to_shorthand}.should == [
+      '2s','2e'
+      ]
+  end
+end