bio-velvet 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: ce80f5a1d0ae5443ab707f1cd93efa576ab27fcf
+  metadata.gz: f88fe95bdfceafceb78b65c763675780ee12f1cf
+  data.tar.gz: 40f0b257c9e15ca861c844a51dbce319ee17453b
 SHA512:
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+  metadata.gz: d4de2138c28eb006fd872e518f7aa5172c04016aded296aeca1bdbeb27e98c7b99fa6f64b5fcf2252c0eff7dacccf08d9b2b4db3e38f05256d12b270cbc3fe19
+  data.tar.gz: f2fe259725937d1995f5a0269a3b6a3a2c3a55b8ecb30abc8e7f54dadfe6311a4d43a3df3bd588c49f3567a7ca9a1846885f0d51bbfb6d66bd84e3cf3b00937c

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/lib/bio-velvet.rb

@@ -11,3 +11,4 @@ end
 
 require 'bio-velvet/graph'
 require 'bio-velvet/runner'
+require 'bio-velvet/sequences'

data/lib/bio-velvet/graph.rb

@@ -1,5 +1,6 @@
 require 'hopcsv'
 require 'bio'
+require 'tempfile'
 
 module Bio
   module Velvet
@@ -32,6 +33,13 @@ module Bio
       # * :interesting_read_ids: If not nil, is a Set of nodes that we are interested in. Reads
       # not of interest will not be parsed in (the NR part of the velvet LastGraph file). Regardless all
       # nodes and edges are parsed in. Using this options saves both memory and CPU.
+      # * :interesting_node_ids: like :interesting_read_ids except it allows targeting of particular nodes
+      # rather than particular reads.
+      # * :grep_hack: to make the parsing of read associations go even faster, a grep-based, rather
+      # hacky method is applied to the graph file, so only NR data of interesting_read_ids is presented
+      # to the parser. This can save days of parsing time, but is a bit of a hack and its usage may
+      # not be particularly future-proof. The value of this option is the amount of context coming out of grep
+      # (the -A and -B flags). Using 500 should probably work for most circumstances, if not an Exception will be raised.
       def self.parse_from_file(path_to_graph_file, options={})
         graph = self.new
         state = :header
@@ -122,17 +130,26 @@ module Bio
             # $READ_ID2 etc.
             #p row
             if row[0] == 'NR'
-              raise unless row.length == 3
-              node_pm = row[1].to_i
-              current_node_direction = node_pm > 0
-              current_node = graph.nodes[node_pm.abs]
-              current_node.number_of_short_reads ||= 0
-              current_node.number_of_short_reads += row[2].to_i
-              next
+              if options[:grep_hack]
+                unless options[:interesting_read_ids] or options[:interesting_node_ids]
+                  raise "Programming error using bio-velvet: if :grep_hack is specified, then :interesting_read_ids or :interesting_node_ids must also be"
+                end
+                apply_grep_hack graph, path_to_graph_file, options[:interesting_read_ids], options[:interesting_node_ids], options[:grep_hack]
+                break #no more parsing is required
+              else
+                raise unless row.length == 3
+                node_pm = row[1].to_i
+                current_node_direction = node_pm > 0
+                current_node = graph.nodes[node_pm.abs]
+                current_node.number_of_short_reads ||= 0
+                current_node.number_of_short_reads += row[2].to_i
+                next
+              end
             else
               raise unless row.length == 3
               read_id = row[0].to_i
-              if options[:interesting_read_ids] and !options[:interesting_read_ids].include?(read_id)
+              if (options[:interesting_node_ids] and !options[:interesting_node_ids].include?(current_node.node_id)) or
+                (options[:interesting_read_ids] and !options[:interesting_read_ids].include?(read_id))
                 # We have come across an uninteresting read. Ignore it.
                 next
               end
@@ -224,6 +241,33 @@ module Bio
         return deleted_nodes, deleted_arcs.flatten
       end
 
+      # Add more noded reads to this already parsed graph. There is
+      # no gaurantee that old NodedRead information is preserved, or removed.
+      #
+      # Options:
+      # * :interesting_read_ids: If not nil, is a Set of nodes that we are interested in. Reads
+      # not of interest will not be parsed in (the NR part of the velvet LastGraph file). Regardless all
+      # nodes and edges are parsed in. Using this options saves both memory and CPU.
+      # * :interesting_node_ids: like :interesting_read_ids except it allows targeting of particular nodes
+      # rather than particular reads.
+      # * :grep_hack: to make the parsing of read associations go even faster, a grep-based, rather
+      # hacky method is applied to the graph file, so only NR data of interesting_read_ids is presented
+      # to the parser. This can save days of parsing time, but is a bit of a hack and its usage may
+      # not be particularly future-proof. The value of this option is the amount of context coming out of grep
+      # (the -A and -B flags). Using 500 should probably work for most circumstances, if not an Exception will be raised.
+      def parse_additional_noded_reads(path_to_graph_file, options)
+        grep_context = options[:grep_hack]
+        if grep_context.nil?
+          raise "Calling Graph#parse_additional_noded_reads without specifying :grep_hack is currently not implemented"
+        end
+        self.class.apply_grep_hack(self,
+          path_to_graph_file,
+          options[:interesting_read_ids],
+          options[:interesting_node_ids],
+          grep_context
+          )
+      end
+
 
 
 
@@ -522,6 +566,97 @@ module Bio
       class NodedRead
         attr_accessor :read_id, :offset_from_start_of_node, :start_coord, :direction
       end
+
+      private
+      def self.apply_grep_hack(graph, path_to_graph_file, interesting_read_ids, interesting_node_ids, grep_context)
+        interesting_read_ids ||= []
+        interesting_node_ids ||= []
+        if interesting_read_ids.empty? and interesting_node_ids.empty?
+          log.debug "Nothing to grep for in grep hack" if log.debug?
+          return
+        end
+
+        Tempfile.open('grep_v_hack') do |tempfile|
+          # Create a file to pass to grep -f
+          unless interesting_read_ids.nil?
+            interesting_read_ids.each do |read_id|
+              tempfile.puts "^#{read_id}\t"
+            end
+          end
+          unless interesting_node_ids.nil?
+            interesting_node_ids.each do |node_id|
+              tempfile.puts "^NR\t#{node_id}\t"
+              tempfile.puts "^NR\t-#{node_id}\t"
+            end
+          end
+          tempfile.close
+
+          cmd = "grep -B #{grep_context.inspect} -A #{grep_context.inspect} -f #{tempfile.path} #{path_to_graph_file.inspect}"
+          # TODO: make this call more robust
+          # grep_result = Bio::Commandeer.run cmd
+          s, grep_result, stderr = systemu cmd
+
+          # Parse the grepped out results
+          current_node = nil
+          current_node_direction = nil
+          in_nr_section = false
+          grep_result.each_line do |line|
+            row = line.split("\t")
+            if in_nr_section == false
+              # If there is a lot of context then the context includes ARC definitions etc. Skip past this.
+              if row[0] == 'NR'
+                in_nr_section = true
+              elsif row[0] == '--'
+                raise "Parsing exception - grep hack too hacky. Sorry. Try modifying the code to increase the default amount of context grep is giving"
+              else
+                next #skip to next line, waiting to ge into NR section
+              end
+            end
+
+            if line == "--\n" #the break introduced by grep
+              # If we encounter a grep break, but haven't assigned any nodes, then that's not good enough
+              if current_node.nil?
+                raise "Parsing exception - grep hack too hacky. Sorry. Try modifying the code to increase the default amount of context grep is giving"
+              end
+              # reset the parsing situation
+              current_node = nil
+            elsif row[0] == 'NR'
+              raise unless row.length == 3
+              node_pm = row[1].to_i
+              current_node_direction = node_pm > 0
+              current_node = graph.nodes[node_pm.abs]
+              current_node.number_of_short_reads ||= 0
+              current_node.number_of_short_reads += row[2].to_i
+              next
+            else
+              raise unless row.length == 3
+              read_id = row[0].to_i
+              if (current_node.nil? or !interesting_node_ids.include?(current_node.node_id)) and
+                !interesting_read_ids.include?(read_id)
+                # We have come across an uninteresting read. Ignore it.
+                next
+              end
+              if current_node.nil?
+                # Came across a high coverage node, and grep isn't giving enough context. Hopefully this won't happen much
+                # particularly if the reads you are interested in are given to velvet first
+                raise "Parsing exception - grep hack too hacky. Sorry. Try modifying the code to increase the default amount of context grep is giving"
+              end
+              nr = NodedRead.new
+              nr.read_id = read_id
+              nr.offset_from_start_of_node = row[1].to_i
+              nr.start_coord = row[2].to_i
+              nr.direction = current_node_direction
+              current_node.short_reads ||= []
+              current_node.short_reads.push nr
+              next
+            end
+          end
+
+          if current_node.nil?
+            raise "Parsing exception - grep hack too hacky. Sorry. Try modifying the code to increase the default amount of context grep is giving"
+          end
+        end
+      end
     end
   end
 end

data/lib/bio-velvet/runner.rb

@@ -85,7 +85,7 @@ module Bio
       # Return a Bio::Velvet::Graph object built from the LastGraph file.
       # The options for parsing are as per Bio::Velvet::Graph#parse_from_file
       def last_graph(options=nil)
-        Bio::Velvet::Graph.parse_from_file(last_graph_path)
+        Bio::Velvet::Graph.parse_from_file(last_graph_path, options)
       end
     end
   end

data/lib/bio-velvet/sequences.rb

@@ -0,0 +1,121 @@
+require 'hopcsv'
+require 'bio'
+require 'tempfile'
+
+module Bio
+  module Velvet
+    # Parser and container class for textual Sequence files
+    #
+    # After parsing, the result is a hash of read_id => sequence
+    # where read_id is an Integer and sequence a String
+    #
+    # The definition of this file is given in the velvet manual, at
+    # http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
+    class Sequences < Hash
+      include Bio::Velvet::Logging
+
+      def self.log
+        self.new.log
+      end
+
+      # Options:
+      # * :interesting_read_ids: If not nil, is a Set of nodes that we are interested in. Reads
+      # not of interest will not be parsed in (the NR part of the velvet LastGraph file). Regardless all
+      # nodes and edges are parsed in. Using this options saves both memory and CPU.
+      # * :grep_hack: to make the parsing of read associations go even faster, a grep-based, rather
+      # hacky method is applied to the graph file, so only sequence data of interesting_read_ids is presented
+      # to the parser. This can save days of parsing time, but is a bit of a hack and its usage may
+      # not be particularly future-proof. The value of this option is the amount of context coming out of grep
+      # (the -A flag). In the Sequence file the sequences are wrapped at 60 characters, so you'll need at
+      # least (longest_sequence_length / 60) + 2 amount of context. The reason for adding 2 is that the
+      # parser will then be able to detect insufficient context and raise an Exception, without
+      # throwing up false positive Exceptions.
+      def self.parse_from_file(path_to_sequence_file, options={})
+        seq_object = Bio::Velvet::Sequences.new
+
+        if options[:apply_grep_hack]
+          apply_grep_hack(seq_object, path_to_sequence_file, options[:interesting_read_ids], options[:apply_grep_hack])
+        else
+          # Parse all the sequences
+          Bio::FlatFile.foreach(path_to_sequence_file) do |seq|
+            read_id = seq.definition.split("\t")[1].to_i
+            if options[:interesting_read_ids].nil? or options[:interesting_read_ids].include?(read_id)
+              seq_object[read_id] = seq.seq.to_s
+            end
+          end
+        end
+        log.info "Read in #{seq_object.length} velvet stored sequences"
+        return seq_object
+      end
+
+      private
+      # Add the interesting sequences to the hash
+      def self.apply_grep_hack(seq_object, path_to_sequence_file, interesting_read_ids, grep_context)
+        return if interesting_read_ids.nil? or interesting_read_ids.empty?
+
+        Tempfile.open('grep_v_hack') do |tempfile|
+          # Create a file to pass to grep -f
+          unless interesting_read_ids.nil?
+            interesting_read_ids.each do |read_id|
+              tempfile.puts "\t#{read_id}\t" #the read_id is the second field of the header
+            end
+          end
+          tempfile.close
+
+          cmd = "grep -F -A #{grep_context.inspect} -f #{tempfile.path} #{path_to_sequence_file.inspect}"
+          # TODO: make this call more robust
+          # grep_result = Bio::Commandeer.run cmd
+          s, grep_result, stderr = systemu cmd
+
+          # Parse the grepped out results
+          current_read_id = nil
+          current_seq = nil
+          last_sequence_line_length = nil
+
+          add_last_sequence = lambda do
+            if current_read_id
+              seq_object[current_read_id] = current_seq
+            end
+          end
+          grep_result.each_line do |line|
+            line.chomp!
+            if line[0] == '>'
+              # Process the last sequence
+              add_last_sequence.call unless current_read_id.nil?
+
+              # Assume the real sequence name contains no tabs
+              read_id = line.split("\t")[1]
+              raise "Unable to parse velvet Sequence file at this line #{line}" if read_id.nil?
+              read_id = read_id.to_i
+              if interesting_read_ids.include?(read_id)
+                # if current_read_id is nil, then we know we are uninterested in this sequence
+                current_read_id = read_id
+              else
+                current_read_id = nil
+              end
+              current_seq = nil
+            elsif line == '--'
+              # grep demarker.
+              add_last_sequence.call unless current_read_id.nil?
+              if last_sequence_line_length == 60
+                raise "Parsing exception when parsing velvet Sequence file - grep hack too hacky. Sorry. Try modifying the code to increase the default amount of context grep is giving"
+              end
+            else
+              # plain old sequence
+              unless current_read_id.nil?
+                current_seq ||= ''
+                current_seq += line
+                last_sequence_line_length = line.length
+              end
+            end
+          end
+          # process the last sequence
+          if last_sequence_line_length == 60
+            raise "Parsing exception when parsing velvet Sequence file at the end of the file - grep hack too hacky. Sorry. Try modifying the code to increase the default amount of context grep is giving"
+          end
+          add_last_sequence.call
+        end
+      end
+    end
+  end
+end

data/spec/bio-velvet_graph_spec.rb

@@ -66,7 +66,7 @@ describe "BioVelvet" do
     # 49981	0	0
     node = graph.nodes[967]
     node.short_reads.nil?.should eq(false)
-    node.short_reads.length.should eq(2), node.inspect
+    node.short_reads.length.should eq(2)
     node.short_reads[0].read_id.should eq(49982)
     node.short_reads[0].offset_from_start_of_node.should eq(0)
     node.short_reads[0].start_coord.should eq(0)
@@ -118,6 +118,142 @@ describe "BioVelvet" do
     node.short_reads[0].offset_from_start_of_node.should eq(41)
   end
 
+  it 'should be able to parse a read tracked graph, using the grep hack correct context' do
+    graph = Bio::Velvet::Graph.parse_from_file(
+      File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2'),
+      {:interesting_read_ids => Set.new([47223]),
+      :grep_hack => 5}
+    )
+    graph.should be_kind_of(Bio::Velvet::Graph)
+
+    graph.number_of_nodes.should eq(967)
+    graph.number_of_sequences.should eq(50000)
+    graph.hash_length.should eq(31)
+
+    # NR	-951	2
+    #47210	0	0
+    #47223	41	0
+    # ====later
+    # NR	951	2
+    # 47209	54	0
+    # 47224	0	0
+    node = graph.nodes[951]
+    node.short_reads.length.should eq(1)
+    # node.number_of_short_reads.should eq(4) #all bets off on this now, because not everything is aprsed
+    node.short_reads[0].read_id.should eq(47223)
+    node.short_reads[0].offset_from_start_of_node.should eq(41)
+  end
+
+  it 'should be able to parse a read tracked graph, using the grep hack context beyond NR' do
+    graph = Bio::Velvet::Graph.parse_from_file(
+      File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2'),
+      {:interesting_read_ids => Set.new([47224]),
+      :grep_hack => 500}
+    )
+    graph.should be_kind_of(Bio::Velvet::Graph)
+
+    graph.number_of_nodes.should eq(967)
+    graph.number_of_sequences.should eq(50000)
+    graph.hash_length.should eq(31)
+
+    # NR	-951	2
+    #47210	0	0
+    #47223	41	0
+    # ====later
+    # NR	951	2
+    # 47209	54	0
+    # 47224	0	0
+    node = graph.nodes[951]
+    node.short_reads.length.should eq(1)
+    # node.number_of_short_reads.should eq(4) #all bets off on this now, because not everything is aprsed
+    node.short_reads[0].read_id.should eq(47224)
+    node.short_reads[0].offset_from_start_of_node.should eq(0)
+  end
+
+  it 'should be able to parse a read tracked graph, using the grep hack insufficient context' do
+    expect {Bio::Velvet::Graph.parse_from_file(
+      File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2'),
+      {:interesting_read_ids => Set.new([47224]),
+      :grep_hack => 0}
+    )}.to raise_error
+  end
+
+  it 'should grep target nodes with grep hack' do
+    graph = Bio::Velvet::Graph.parse_from_file(
+      File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2'),
+      {:interesting_node_ids => Set.new([951]),
+      :grep_hack => 500}
+    )
+    graph.should be_kind_of(Bio::Velvet::Graph)
+
+    graph.number_of_nodes.should eq(967)
+    graph.number_of_sequences.should eq(50000)
+    graph.hash_length.should eq(31)
+
+    # NR	-951	2
+    #47210	0	0
+    #47223	41	0
+    # ====later
+    # NR	951	2
+    # 47209	54	0
+    # 47224	0	0
+    node = graph.nodes[951]
+    node.short_reads.length.should eq(4)
+    node.short_reads.collect{|r| r.read_id}.should == [47210, 47223, 47209, 47224]
+    node.short_reads[0].offset_from_start_of_node.should eq(0)
+  end
+
+  it 'should grep target nodes without grep hack' do
+    graph = Bio::Velvet::Graph.parse_from_file(
+      File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2'),
+      {:interesting_node_ids => Set.new([951])}
+    )
+    graph.should be_kind_of(Bio::Velvet::Graph)
+
+    graph.number_of_nodes.should eq(967)
+    graph.number_of_sequences.should eq(50000)
+    graph.hash_length.should eq(31)
+
+    # NR	-951	2
+    #47210	0	0
+    #47223	41	0
+    # ====later
+    # NR	951	2
+    # 47209	54	0
+    # 47224	0	0
+    node = graph.nodes[951]
+    node.short_reads.length.should eq(4)
+    node.short_reads.collect{|r| r.read_id}.should == [47210, 47223, 47209, 47224]
+    node.short_reads[0].offset_from_start_of_node.should eq(0)
+  end
+
+  it 'should parse_additional_noded_reads with interesting_node_ids' do
+    graph_file = File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2')
+    graph = Bio::Velvet::Graph.parse_from_file(
+      graph_file,
+      {:interesting_node_ids => [] }
+    )
+    graph.nodes[951].short_reads.should == nil
+
+    graph.parse_additional_noded_reads(graph_file, :interesting_node_ids => [951], :grep_hack => 500)
+    node = graph.nodes[951]
+    node.short_reads.length.should eq(4)
+    node.short_reads.collect{|r| r.read_id}.should == [47210, 47223, 47209, 47224]
+  end
+
+  it 'should parse_additional_noded_reads with interesting_read_ids' do
+    graph_file = File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2')
+    graph = Bio::Velvet::Graph.parse_from_file(
+      graph_file,
+      {:interesting_node_ids => [] }
+    )
+    graph.nodes[951].short_reads.should == nil
+
+    graph.parse_additional_noded_reads(graph_file, :interesting_read_ids => [47210], :grep_hack => 2)
+    node = graph.nodes[951]
+    node.short_reads.collect{|r| r.read_id}.should == [47210]
+  end
+
   it 'should return sets of arcs by id' do
     graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly','LastGraph')
     #    ARC     2       -578    1

data/spec/data/sequence_spec/5seqs.fa

@@ -0,0 +1,24 @@
+>1_1
+CAGCACCTGTGCTGGCGCTCCGAAGAGGGGCCGATGTTTCCACCGGCTTGCACCAGCATGTCAAGCCCAGGTAAGGTTCTTCGCGTTGCTTCGAATTAAA
+>1_2
+AGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGTGGCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGT
+>2_1
+AGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTGGCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACGGCCGG
+>2_2
+GGAGTTGAGCCCCGGGATTTCACCAGCCACTTAACGGGCCACCTACGCGCCCTTTACGCCCAGTGATTCCGGACAACGCTCGCACCCTCCGTATTACCGC
+>3_1
+AGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCAAGCCGGTG
+>3_2
+CCGGCTTCCATGGCGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGGCTGATCCGCGATTACTAGCGATTCCGGCTTCATGCCG
+>4_1
+AGGTGGCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGCGAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCG
+>4_2
+CGGCAGTCCCCCCAGAGTCCCCGGCCGAACCGCTGGCAACTGGGAGCGAGAGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGAC
+>5_1
+ACGGGCCACCTACGCGCCCTTTACGCCCAGTGATTCCGGACAACGCTCGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTCCTT
+>5_2
+GCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACGGCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTG
+>6_1
+GGGTAACGGCCCACCAAGGCGACGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAG
+>6_2
+CGGGAATTCCATCTGCCCCTACCGTGCTCTAGCTCGCCAGTCTGACCGGCAGCCCCGGAGTTGAGCCCCGGGATTTCACCAGCCACTTAACGGGCCACCT

data/spec/data/sequence_spec/5seqs.fa.Sequences

@@ -0,0 +1,36 @@
+>1_1	1	0
+CAGCACCTGTGCTGGCGCTCCGAAGAGGGGCCGATGTTTCCACCGGCTTGCACCAGCATG
+TCAAGCCCAGGTAAGGTTCTTCGCGTTGCTTCGAATTAAA
+>1_2	2	0
+AGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGTGGCCCGTTAAGT
+GGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGT
+>2_1	3	0
+AGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTGGCAGACGGGTGCGTAACACGTGAGC
+AACTTGTCCGACGGCGGGGGATAGCCGGCCCAACGGCCGG
+>2_2	4	0
+GGAGTTGAGCCCCGGGATTTCACCAGCCACTTAACGGGCCACCTACGCGCCCTTTACGCC
+CAGTGATTCCGGACAACGCTCGCACCCTCCGTATTACCGC
+>3_1	5	0
+AGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGA
+AGAACCTTACCTGGGCTTGACATGCTGGTGCAAGCCGGTG
+>3_2	6	0
+CCGGCTTCCATGGCGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCG
+TGGCTGATCCGCGATTACTAGCGATTCCGGCTTCATGCCG
+>4_1	7	0
+AGGTGGCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGA
+CTGGCGAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCG
+>4_2	8	0
+CGGCAGTCCCCCCAGAGTCCCCGGCCGAACCGCTGGCAACTGGGAGCGAGAGTTGCGCTC
+GTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGAC
+>5_1	9	0
+ACGGGCCACCTACGCGCCCTTTACGCCCAGTGATTCCGGACAACGCTCGCACCCTCCGTA
+TTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTCCTT
+>5_2	10	0
+GCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACG
+GCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTG
+>6_1	11	0
+GGGTAACGGCCCACCAAGGCGACGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATT
+GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAG
+>6_2	12	0
+CGGGAATTCCATCTGCCCCTACCGTGCTCTAGCTCGCCAGTCTGACCGGCAGCCCCGGAG
+TTGAGCCCCGGGATTTCACCAGCCACTTAACGGGCCACCT

data/spec/data/sequence_spec/Sequences

@@ -0,0 +1,18 @@
+>read1	1	0
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
+CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
+ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
+GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
+ACTATGCTGGTATTTCACTTCCAGGTACAGG
+>read2	2	0
+ACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTCCTAAAGGGTATAGC
+CTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTAT
+ACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAAT
+ATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATT
+TCACTTCCAGGTACAGGTGGAATTGGAACAGATGGATTCATTAAAATAGGGCTAGTTTTA
+TTAGGGGTTGTTATTATTCTAGGTGCAGGATATGTTGTCTTAGATAAAAGAAAGAGAATT
+TAATTAAATAAAAATATACTTCTTCTATTTTTAT

data/spec/sequences_spec.rb

@@ -0,0 +1,113 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio'
+
+class String
+  def revcom
+    Bio::Sequences::NA.new(self).reverse_complement.to_s.upcase
+  end
+end
+
+seq1_sequence = 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
+CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
+ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
+GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
+ACTATGCTGGTATTTCACTTCCAGGTACAGG'.gsub("\n",'')
+seq2_sequence = 'ACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTCCTAAAGGGTATAGC
+CTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTAT
+ACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAAT
+ATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATT
+TCACTTCCAGGTACAGGTGGAATTGGAACAGATGGATTCATTAAAATAGGGCTAGTTTTA
+TTAGGGGTTGTTATTATTCTAGGTGCAGGATATGTTGTCTTAGATAAAAGAAAGAGAATT
+TAATTAAATAAAAATATACTTCTTCTATTTTTAT'.gsub("\n",'')
+
+describe "BioVelvet" do
+  it "should be able to parse a whole Sequences file" do
+    seqs = Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','Sequences')
+    seqs.should be_kind_of(Bio::Velvet::Sequences)
+    seqs.should be_kind_of(Hash)
+    seqs.keys.should == [1,2]
+    seqs[1].should == seq1_sequence
+    seqs[2].should == seq2_sequence
+  end
+
+  it 'should be able to read in an interesting seq only' do
+    seqs = Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','Sequences'),
+    :interesting_read_ids => [1]
+    seqs.keys.should == [1]
+    seqs = Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','Sequences'),
+    :interesting_read_ids => [2]
+    seqs.keys.should == [2]
+    seqs = Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','Sequences'),
+    :interesting_read_ids => [1,2]
+    seqs.keys.should == [1,2]
+    seqs[1].should == seq1_sequence
+  end
+
+  it 'should be able to apply the grep hack' do
+    seqs = Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','Sequences'),
+    {:interesting_read_ids => [1], :apply_grep_hack => 500}
+    seqs.keys.should == [1]
+    seqs[1].should == seq1_sequence
+  end
+
+  it 'should be able to apply the grep hack when there is only just enough context' do
+    seqs = Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','Sequences'),
+    {:interesting_read_ids => [1], :apply_grep_hack => 9}
+    seqs.keys.should == [1]
+    seqs[1].should == seq1_sequence
+  end
+
+  it 'should warn when insufficient context is given' do
+    expect {
+      Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','Sequences'),
+      {:interesting_read_ids => [1], :apply_grep_hack => 8}
+      }.to raise_error
+  end
+
+  it 'should be able to handle multiple separated read ids with the grep hack' do
+    s = Bio::Velvet::Sequences.parse_from_file File.join(TEST_DATA_DIR, 'sequence_spec','5seqs.fa.Sequences')
+    s = ['']+s.values
+    seq_file = File.join(TEST_DATA_DIR, 'sequence_spec','5seqs.fa.Sequences')
+
+    seqs = Bio::Velvet::Sequences.parse_from_file seq_file,
+    {:interesting_read_ids => [1], :apply_grep_hack => 9}
+    seqs.keys.should == [1]
+    seqs[1].should == s[1]
+
+    seqs = Bio::Velvet::Sequences.parse_from_file seq_file,
+    {:interesting_read_ids => [1,2], :apply_grep_hack => 9}
+    seqs.keys.should == [1,2]
+    seqs.values.should == s[1..2]
+
+    seqs = Bio::Velvet::Sequences.parse_from_file seq_file,
+    {:interesting_read_ids => [1,2], :apply_grep_hack => 2}
+    seqs.keys.should == [1,2]
+    seqs.values.should == s[1..2]
+
+    seqs = Bio::Velvet::Sequences.parse_from_file seq_file,
+    {:interesting_read_ids => [1,5], :apply_grep_hack => 2}
+    seqs.keys.should == [1,5]
+    seqs.values.should == [s[1],s[5]]
+
+    seqs = Bio::Velvet::Sequences.parse_from_file seq_file,
+    {:interesting_read_ids => [1,5], :apply_grep_hack => 3}
+    seqs.keys.should == [1,5]
+    seqs.values.should == [s[1],s[5]]
+
+    seqs = Bio::Velvet::Sequences.parse_from_file seq_file,
+    {:interesting_read_ids => [1,12], :apply_grep_hack => 3}
+    seqs.keys.should == [1,12]
+    seqs.values.should == [s[1],s[12]]
+
+    expect {
+      seqs = Bio::Velvet::Sequences.parse_from_file seq_file,
+      {:interesting_read_ids => [12], :apply_grep_hack => 1}
+      seqs.keys.should == [1,12]
+      seqs.values.should == [s[1],s[12]]
+      }.to raise_error
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-06 00:00:00.000000000 Z
+date: 2014-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
@@ -155,12 +155,16 @@ files:
 - lib/bio-velvet.rb
 - lib/bio-velvet/graph.rb
 - lib/bio-velvet/runner.rb
+- lib/bio-velvet/sequences.rb
 - spec/bio-velvet_arc_array_spec.rb
 - spec/bio-velvet_graph_spec.rb
 - spec/bio-velvet_runner_spec.rb
 - spec/data/node_sequence/LastGraph
 - spec/data/node_sequence/contigs.fa
 - spec/data/runner_input.fa
+- spec/data/sequence_spec/5seqs.fa
+- spec/data/sequence_spec/5seqs.fa.Sequences
+- spec/data/sequence_spec/Sequences
 - spec/data/short_node_LastGraph
 - spec/data/short_node_sequence_test_graph
 - spec/data/velvet_test_reads_assembly/Graph
@@ -169,6 +173,7 @@ files:
 - spec/data/velvet_test_reads_assembly_read_tracking/Graph2
 - spec/data/velvet_test_reads_assembly_read_tracking/HOWTO_RECREATE
 - spec/data/velvet_test_trail_sequence_assembly/reads1.fa
+- spec/sequences_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/wwood/bioruby-velvet
 licenses:
@@ -190,7 +195,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.0
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Parser to work with file formats used in the velvet DNA assembler