bio-velvet_underground 0.2.1 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: f3898e399d3ff7c44e6ebcb37920be2a119603e2
+  metadata.gz: f1ae3ddf8e6093e4808984c2a525a633cd6b7a3d
+  data.tar.gz: e36bd5e26e2f89d2f5917e5333e4420d0817e180
 SHA512:
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+  metadata.gz: 457377686af6d3344811f1d9acb0b4c3153842dde4bc36b1c1e7f2802ec0577132a1db7c6a0237db73f8ff870d6d2ef0c992d36f4f9c726720e64c0f48e9b0d5
+  data.tar.gz: f59ba0ee02ecc7239c82750c4bc17d1d851a29818a55158f853a337aeb89be23fca20112213a6822434d813e2af0ba10bf91f333448e1d78f1db6e402808e7f7

data/Gemfile

@@ -5,6 +5,7 @@ source "http://rubygems.org"
 
 gem 'ffi', '~> 1.9'
 gem 'bio-logger', '~> 1.0'
+gem 'bio-velvet', '~> 0.6'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.3.0

data/lib/bio-velvet_underground/binary_sequence_store.rb

@@ -55,6 +55,12 @@ class Bio::Velvet::Underground
         sequence_id+1
       end
     end
+
+    # Return the number of libraries used in this sequence store that were paired-end
+    # e.g.
+    def num_paired_end_readsets
+      Bio::Velvet::Underground.pairedCategories(@readset)
+    end
   end
 
   private

data/lib/bio-velvet_underground/graph.rb

@@ -1,4 +1,5 @@
 require 'csv'
+require 'bio-velvet'
 
 class Bio::Velvet::Underground
 
@@ -34,7 +35,7 @@ class Bio::Velvet::Underground
     end
 
     def nodes
-      NodeArray.new self
+      @nodes ||= NodeArray.new self #cache node array
     end
 
     def node_count
@@ -51,6 +52,7 @@ class Bio::Velvet::Underground
 
       def initialize(graph)
         @graph = graph
+        @node_cache = []
       end
 
       def each
@@ -64,10 +66,13 @@ class Bio::Velvet::Underground
       end
 
       def [](node_id)
+        cache = @node_cache[node_id]
+        return cache unless cache.nil?
+
         return nil if node_id < 1 or node_id > @graph.internal_graph_struct[:nodeCount]
         pointer = Bio::Velvet::Underground.getNodeInGraph @graph.internal_graph_struct, node_id
         node_struct = Bio::Velvet::Underground::NodeStruct.new pointer
-        Node.new(@graph, node_struct)
+        @node_cache[node_id] = Node.new(@graph, node_struct)
       end
     end
 
@@ -80,11 +85,11 @@ class Bio::Velvet::Underground
       end
 
       def node_id
-        @internal_node_struct[:ID]
+        @node_id ||= @internal_node_struct[:ID]
       end
 
       def length_alone
-        @internal_node_struct[:length]
+        @length_alone ||= @internal_node_struct[:length]
       end
 
       def coverages
@@ -95,13 +100,14 @@ class Bio::Velvet::Underground
       end
 
       def ends_of_kmers_of_node
+        return @ends_of_kmers_of_node unless @ends_of_kmers_of_node.nil?
         seq = []
         key = %w(A C G T)
         0.upto(length_alone-1) do |i|
           n = Bio::Velvet::Underground.getNucleotideInNode(@internal_node_struct, i)
           seq.push key[n]
         end
-        return seq.join
+        @ends_of_kmers_of_node = seq.join
       end
 
       def ends_of_kmers_of_twin_node
@@ -123,10 +129,13 @@ class Bio::Velvet::Underground
         array_start_pointer = Bio::Velvet::Underground.getNodeReads @internal_node_struct, @graph.internal_graph_struct
         num_short_reads = Bio::Velvet::Underground.getNodeReadCount @internal_node_struct, @graph.internal_graph_struct
         struct_size = Bio::Velvet::Underground::ShortReadMarker.size #calculate once for performance
-        @short_reads = 0.step(num_short_reads-1, 1).collect do |i|
+
+        # Return a hash of read_id => short_read object
+        @short_reads = Bio::Velvet::Graph::NodedReadArray.new
+        0.step(num_short_reads-1, 1).each do |i|
           # Use the fact that FFI pointers can do pointer arithmetic
           pointer = array_start_pointer+(i*struct_size)
-          NodedRead.new Bio::Velvet::Underground::ShortReadMarker.new(pointer), true
+          @short_reads.push(NodedRead.new(Bio::Velvet::Underground::ShortReadMarker.new(pointer), true))
         end
         return @short_reads
       end
@@ -136,12 +145,13 @@ class Bio::Velvet::Underground
       end
 
       def short_reads
-        reads = fwd_short_reads
+        return @reads unless @reads.nil?
+        @reads = fwd_short_reads
         rev_short_reads.each do |read|
           read.direction = false
-          reads.push read
+          @reads.push read
         end
-        return reads
+        return @reads
       end
     end
 
@@ -165,15 +175,15 @@ class Bio::Velvet::Underground
       end
 
       def read_id
-        @internal_short_read_struct[:readID]
+        @read_id ||= @internal_short_read_struct[:readID]
       end
 
       def offset_from_start_of_node
-        @internal_short_read_struct[:position]
+        @offset_from_start_of_node ||= @internal_short_read_struct[:position]
       end
 
       def start_coord
-        @internal_short_read_struct[:offset]
+        @start_coord ||= @internal_short_read_struct[:offset]
       end
     end
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet_underground
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
 platform: ruby
 authors:
 - Ben Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-05 00:00:00.000000000 Z
+date: 2015-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -38,6 +38,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: bio-velvet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement