bio-velvet_underground 0.0.1 → 0.1.0

data/spec/data/3/Assem/Log

@@ -0,0 +1,42 @@
+Thu Apr 17 13:20:41 2014
+ /srv/whitlam/home/users/uqbwoodc/git/bioruby-velvet_underground/ext/src/velveth Assem 31 -short -fasta Sequences
+Version 1.2.10
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 31
+
+Thu Apr 17 13:20:58 2014
+ /srv/whitlam/home/users/uqbwoodc/git/bioruby-velvet_underground/ext/src/velvetg Assem
+Version 1.2.10
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 31
+
+Final graph has 4 nodes and n50 of 224, max 228, total 519, using 0/5 reads
+Thu Apr 17 13:21:17 2014
+ /srv/whitlam/home/users/uqbwoodc/git/bioruby-velvet_underground/ext/src/velveth Assem 31 -short -fasta Sequences -read_trkg yes
+Version 1.2.10
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 31
+
+Thu Apr 17 13:21:53 2014
+ /srv/whitlam/home/users/uqbwoodc/git/bioruby-velvet_underground/ext/src/velvetg Assem -read_trkg yes
+Version 1.2.10
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 31
+
+Final graph has 4 nodes and n50 of 224, max 228, total 519, using 5/5 reads

data/spec/data/3/Assem/PreGraph

@@ -0,0 +1,9 @@
+4	5	31	1
+NODE	1	228
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG
+NODE	2	29
+CTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAA
+NODE	3	224
+GGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
+NODE	4	38
+CTGATAAAAATGGACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAA

data/spec/data/3/Assem/Roadmaps

@@ -0,0 +1,15 @@
+5	0	31	1
+ROADMAP 1
+ROADMAP 2
+1	0	0	228
+1	38	257	481
+ROADMAP 3
+-1	0	480	-1
+ROADMAP 4
+1	0	0	228
+2	0	0	38
+1	0	257	481
+ROADMAP 5
+-1	0	480	256
+-2	0	37	-1
+-1	0	227	-1

data/spec/data/3/Assem/Sequences

@@ -0,0 +1,50 @@
+>1	1	0
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
+CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
+ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
+GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
+ACTATGCTGGTATTTCACTTCCAGGTACAGG
+>2	2	0
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAG
+AAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTC
+AAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATG
+AAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTAC
+AAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
+>NODE_1_length_481_cov_1.471933_revcom	3	0
+CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
+CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
+ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
+ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
+CCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTT
+AATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTA
+TCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTT
+TTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGAT
+TCTAAATCGTGATCTTTGGTAGAGATAAGTG
+>3	4	0
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAG
+AAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTC
+AAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATG
+AAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTAC
+AAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
+>3_revcom	5	0
+CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
+CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
+ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
+ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
+CCTTCTTTTAAACCCCCCCCCGCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCC
+TTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTA
+CCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAA
+TCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTA
+TAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG

data/spec/data/3/Assem/contigs.fa

@@ -0,0 +1,15 @@
+>NODE_1_length_228_cov_5.000000
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTG
+>NODE_3_length_224_cov_5.000000
+GGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTT
+TTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACT
+GGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATT
+ACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCA
+CTTCCAGGTACAGg
+>NODE_4_length_38_cov_3.000000
+CTGATAAAAATGGACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACT
+TTATAAAA

data/spec/data/3/Assem/stats.txt

@@ -0,0 +1,5 @@
+ID	lgth	out	in	long_cov	short1_cov	short1_Ocov	short2_cov	short2_Ocov	long_nb	short1_nb	short2_nb
+1	228	2	0	0.000000	5.000000	5.000000	0.000000	0.000000	0	3	0
+2	29	1	1	0.000000	2.000000	2.000000	0.000000	0.000000	0	1	0
+3	224	0	2	0.000000	5.000000	5.000000	0.000000	0.000000	0	3	0
+4	38	1	1	0.000000	3.000000	3.000000	0.000000	0.000000	0	2	0

data/spec/data/3/Sequences

@@ -0,0 +1,50 @@
+>1	1	0
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
+CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
+ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
+GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
+ACTATGCTGGTATTTCACTTCCAGGTACAGG
+>2	2	0
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAG
+AAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTC
+AAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATG
+AAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTAC
+AAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
+>NODE_1_length_481_cov_1.471933_revcom	3	0
+CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
+CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
+ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
+ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
+CCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTT
+AATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTA
+TCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTT
+TTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGAT
+TCTAAATCGTGATCTTTGGTAGAGATAAGTG
+>3	4	0
+CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
+TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
+ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
+CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
+GACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAG
+AAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTC
+AAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATG
+AAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTAC
+AAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
+>3_revcom	5	0
+CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
+CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
+ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
+ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
+CCTTCTTTTAAACCCCCCCCCGCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCC
+TTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTA
+CCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAA
+TCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTA
+TAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG

data/spec/data/4/LastGraphKmer51Head

@@ -0,0 +1,7 @@
+221	8987	51	1
+NODE	1	236	8451	8451	0	0
+CGCGGCGGCTTGCCTCCGTCTTCATCCAGCGTGTCCGGCTTGAGCGTCCACAAACCGAAGCCGATGAAGAGCACCGCCAGGAGCAGCGCCATCCACTTCGCCGGCACGTGCGCGGACACCCAACTGCCCACGCTGGACGCCAGCGCGTGATTGGCGACGGTGGCGACGAAGATGCCCGCCAGCACATGCCACGGCTTGCGAAACCGCGTGGCCAGGGAGAACGCGAGCAACTGCGT
+TGTGCTGGCGGGCATCTTCGTCGCCACCGTCGCCAATCACGCGCTGGCGTCCAGCGTGGGCAGTTGGGTGTCCGCGCACGTGCCGGCGAAGTGGATGGCGCTGCTCCTGGCGGTGCTCTTCATCGGCTTCGGTTTGTGGACGCTCAAGCCGGACACGCTGGATGAAGACGGAGGCAAGCCGCCGCGCTTCGGCGCTTTCCTCACCACGGTGGTGCTCTTCTTCCTCGCGGAGATGG
+NODE	2	913	31246	31246	0	0
+ACCTTCCGCCTGACGCCGGGGCCGCATCCCGGCCCCGGGTGCCGTGTCGATGCGGCTTCTTACGGGGTGGGCGTCGACGCCTGCTCCGTCTCCGCGGGAGCGGCTCCCGTCTTCGCGGGGGCGGTGTCACCGCTCTTGCCCGTCACCACACCCTTCACCTTCTCCATGGCGGCCTTCGGGTCGATGTTGCCCTTGAGGGTGCCGAACGGCGTGTCGATGACCTGCTCCCGCTTCTCCGAGGAGGCGTAGCCCTCTGGCGCGCACAGGGCCTTCGAGGTGTCGCGCACGGAGACGACGGGGGTGTTGATGGTGGTGGAGTCCTCGGACGTGGCCTTGGCGACGAGCTTGTCGTCGCGCATCAGCACGCAGCGGTCCTCGCCGTAGTACCAGGCGGTGGAGCTGTCCGGGAACTCCTGCGCGCGCGTGGGTCCTGAGCCCATGGCATCGACGACCTGATGGGACGACATGCCCGGGTAGAGCTTGTCGAAGCCAGGGGTGGCACAGCCGGCGGCGGCGAGCGCGAGTGCGGCGCTGACAATCGGGAGACGCATGGGGTGTGGGGCTCCTTCCGAAAAGGAATCGCGGAGCCTACCCCGGCGCCACGTCCGGCCTCCATGTGGGGGGCCGGACGCATCGTGTCAGAGTTCCTGATCCAACCAGCGGACGATGGCCTCGCGAATCGAGGCCGGCCGCTCGGAGTCCAGTCGGGTGCGAAGCAGGCGGGCCGCGTCGGCGTCGCGCAGCATTGAAGCGGGCATCAGCTCACGCGTGCGAGGAAGGGACGCGCGGGACGCGACGGCGGCAGACCTCATGACTGGCCTTCCTCCTTGGGCTCTCCGCGGCCGTACTTGCCGAGCAGGTCATCCACGGCCTCGCGCAGGTACTCGCTCTGGTGGATGCGGGTCCGCCGCGC
+TGACCTGCTCGGCAAGTACGGCCGCGGAGAGCCCAAGGAGGAAGGCCAGTCATGAGGTCTGCCGCCGTCGCGTCCCGCGCGTCCCTTCCTCGCACGCGTGAGCTGATGCCCGCTTCAATGCTGCGCGACGCCGACGCGGCCCGCCTGCTTCGCACCCGACTGGACTCCGAGCGGCCGGCCTCGATTCGCGAGGCCATCGTCCGCTGGTTGGATCAGGAACTCTGACACGATGCGTCCGGCCCCCCACATGGAGGCCGGACGTGGCGCCGGGGTAGGCTCCGCGATTCCTTTTCGGAAGGAGCCCCACACCCCATGCGTCTCCCGATTGTCAGCGCCGCACTCGCGCTCGCCGCCGCCGGCTGTGCCACCCCTGGCTTCGACAAGCTCTACCCGGGCATGTCGTCCCATCAGGTCGTCGATGCCATGGGCTCAGGACCCACGCGCGCGCAGGAGTTCCCGGACAGCTCCACCGCCTGGTACTACGGCGAGGACCGCTGCGTGCTGATGCGCGACGACAAGCTCGTCGCCAAGGCCACGTCCGAGGACTCCACCACCATCAACACCCCCGTCGTCTCCGTGCGCGACACCTCGAAGGCCCTGTGCGCGCCAGAGGGCTACGCCTCCTCGGAGAAGCGGGAGCAGGTCATCGACACGCCGTTCGGCACCCTCAAGGGCAACATCGACCCGAAGGCCGCCATGGAGAAGGTGAAGGGTGTGGTGACGGGCAAGAGCGGTGACACCGCCCCCGCGAAGACGGGAGCCGCTCCCGCGGAGACGGAGCAGGCGTCGACGCCCACCCCGTAAGAAGCCGCATCGACACGGCACCCGGGGCCGGGATGCGGCCCCGGCGTCAGGCGGAAGGTGCCGCCGCCTCGCCGTCCTTGTCGTCCAGCTTGCCGGCGATGTCCTTGAA

data/spec/graph_spec.rb

@@ -0,0 +1,52 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "graph" do
+  it "should be able to load a graph and respond to basic structures" do
+    path = File.join TEST_DATA_DIR, '3', 'Assem', 'LastGraph'
+    graph = Bio::Velvet::Underground::Graph.parse_from_file path
+
+    graph.hash_length.should == 31
+    graph.node_count.should == 4
+  end
+
+  it 'should be able to parse a graph with kmer length > 31, the default' do
+    path = File.join TEST_DATA_DIR, '4', 'LastGraphKmer51Head'
+    graph = Bio::Velvet::Underground::Graph.parse_from_file path
+
+    graph.hash_length.should == 51
+  end
+
+  describe "nodes" do
+    it "should provide basic info" do
+      path = File.join TEST_DATA_DIR, '3', 'Assem', 'LastGraph'
+      graph = Bio::Velvet::Underground::Graph.parse_from_file path
+
+      graph.nodes[1].kind_of?(Bio::Velvet::Underground::Graph::Node).should == true
+      graph.nodes[1].length_alone.should == 228
+      graph.nodes[1].node_id.should == 1
+      graph.nodes[2].kind_of?(Bio::Velvet::Underground::Graph::Node).should == true
+      graph.nodes[2].node_id.should == 2
+      graph.nodes[2].length_alone.should == 29
+      graph.nodes[3].length_alone.should == 224
+      graph.nodes[4].length_alone.should == 38
+      graph.nodes[4].node_id.should == 4
+      graph.nodes[2].coverages.should == [58,0]
+
+      graph.nodes[2].ends_of_kmers_of_node.should == 'GTTTAAAAGAAGGAGATTACTTTATAAAA'
+      graph.nodes[2].ends_of_kmers_of_twin_node.should == 'AGTAAATATAACTCGTCCATTTTTATCAG'
+    end
+
+    it 'should work with short reads' do
+      path = File.join TEST_DATA_DIR, '3', 'Assem', 'LastGraph'
+      graph = Bio::Velvet::Underground::Graph.parse_from_file path
+
+      node = graph.nodes[1]
+      shorts = node.short_reads
+      shorts.length.should == 5
+      shorts.collect{|s| s.direction}.should == [true, true, true, false, false]
+      shorts.collect{|s| s.read_id}.should == [1,2,4,3,5]
+      shorts.collect{|s| s.offset_from_start_of_node}.should == [0,0,0,0,0]
+      shorts.collect{|s| s.start_coord}.should == [0,0,0,253,262]
+    end
+  end
+end

data/spec/runner_spec.rb

@@ -0,0 +1,18 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+require 'tmpdir'
+
+#Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('bio-velvet_underground'); Bio::Log::CLI.configure('bio-velvet_underground')
+describe "runner" do
+  it "should run basic" do
+    reads = File.join TEST_DATA_DIR, '3', 'Sequences'
+    Dir.mktmpdir do |dir|
+      Bio::Velvet::Underground::Runner.run(51,
+      ['-fasta',reads],
+      ['-tour_bus','no'],
+      {:velvet_directory => dir}).should == 0
+
+      File.exist?(File.join(dir, 'contigs.fa')).should == true
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -1,24 +1,9 @@
-require 'simplecov'
-
-module SimpleCov::Configuration
-  def clean_filters
-    @filters = []
-  end
-end
-
-SimpleCov.configure do
-  clean_filters
-  load_adapter 'test_frameworks'
-end
-
-ENV["COVERAGE"] && SimpleCov.start do
-  add_filter "/.rvm/"
-end
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 
 require 'rspec'
 require 'bio-velvet_underground'
+require 'pry'
 
 # Requires supporting files with custom matchers and macros, etc,
 # in ./support/ and its subdirectories.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet_underground
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.1.0
 platform: ruby
 authors:
 - Ben Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-31 00:00:00.000000000 Z
+date: 2014-05-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -24,6 +24,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.9'
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
@@ -147,13 +161,13 @@ extra_rdoc_files:
 files:
 - ".document"
 - ".gitmodules"
+- ".rspec"
 - ".travis.yml"
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
 - VERSION
-- ext/bioruby.patch
 - ext/mkrf_conf.rb
 - ext/src/Makefile
 - ext/src/src/allocArray.c
@@ -424,10 +438,26 @@ files:
 - ext/src/third-party/zlib-1.2.3/zutil.c
 - ext/src/third-party/zlib-1.2.3/zutil.h
 - lib/bio-velvet_underground.rb
+- lib/bio-velvet_underground/binary_sequence_store.rb
+- lib/bio-velvet_underground/constants.rb
 - lib/bio-velvet_underground/external/VERSION
-- lib/bio-velvet_underground/velvet_underground.rb
+- lib/bio-velvet_underground/graph.rb
+- lib/bio-velvet_underground/runner.rb
 - spec/binary_sequence_store_spec.rb
 - spec/data/1/CnyUnifiedSeq
+- spec/data/2/CnyUnifiedSeq
+- spec/data/3/Assem/Graph2
+- spec/data/3/Assem/LastGraph
+- spec/data/3/Assem/Log
+- spec/data/3/Assem/PreGraph
+- spec/data/3/Assem/Roadmaps
+- spec/data/3/Assem/Sequences
+- spec/data/3/Assem/contigs.fa
+- spec/data/3/Assem/stats.txt
+- spec/data/3/Sequences
+- spec/data/4/LastGraphKmer51Head
+- spec/graph_spec.rb
+- spec/runner_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/wwood/bioruby-velvet_underground
 licenses:

data/ext/bioruby.patch

@@ -1,60 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 8239e72..e0308db 100644
---- a/Makefile
-+++ b/Makefile
-@@ -38,16 +38,17 @@ endif
- 
- OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o
- OBJDBG = $(subst obj,obj/dbg,$(OBJ))
-+OBJSHARED = $(subst obj,obj/shared,$(OBJ))
- 
- default : cleanobj zlib obj velveth velvetg doc
- 
- clean : clean-zlib
--	-rm obj/*.o obj/dbg/*.o ./velvet* 
-+	-rm obj/*.o obj/dbg/*.o obj/shared/*.o obj/shared/velvet.so.0.0.1 ./velvet* 
- 	-rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
- 	-rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log
- 
- cleanobj: 
--	-rm obj/*.o obj/dbg/*.o 
-+	-rm obj/*.o obj/dbg/*.o obj/shared/*.o
- 
- ifdef BUNDLEDZLIB
- Z_LIB_DIR=third-party/zlib-1.2.3
-@@ -118,3 +119,15 @@ Manual.pdf: doc/manual_src/Manual.tex doc/manual_src/Columbus_manual.tex
- 
- test: velvetg velveth
- 	cd tests && ./run-tests.sh
-+
-+sharedobjdir:
-+	mkdir -p obj/shared
-+
-+obj/shared: sharedobjdir $(OBJSHARED)
-+
-+obj/shared/%.o: src/%.c
-+	$(CC) -fPIC $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
-+
-+shared: zlib obj/shared
-+	cd obj/shared && gcc -shared -Wl,-soname,libvelvet.so.1 -o libvelvet.so.1.0 allocArray.o autoOpen.o binarySequences.o concatenatedGraph.o concatenatedPreGraph.o correctedGraph.o dfibHeap.o dfib.o fibHeap.o fib.o graph.o graphReConstruction.o graphStats.o kmer.o kmerOccurenceTable.o locallyCorrectedGraph.o passageMarker.o preGraphConstruction.o preGraph.o readCoherentGraph.o readSet.o recycleBin.o roadMap.o scaffold.o shortReadPairs.o splay.o splayTable.o tightString.o utility.o
-+
-diff --git a/src/utility.c b/src/utility.c
-index d402629..126b386 100644
---- a/src/utility.c
-+++ b/src/utility.c
-@@ -97,6 +97,7 @@ void exitErrorf(int exitStatus, boolean showErrno, const char *format, ...)
- 
- void velvetLog(const char *format, ...)
- {
-+/*
-   static boolean timeIsSet = false;
-   static struct timeval tvStart;
-   struct timeval tvNow;
-@@ -120,6 +121,7 @@ void velvetLog(const char *format, ...)
- #ifdef DEBUG 
-   fflush(stdout);
- #endif
-+*/
- }
- 
- void velvetFprintf(FILE * file, const char * format, ...) 

data/lib/bio-velvet_underground/velvet_underground.rb

@@ -1,72 +0,0 @@
-require 'ffi'
-require 'pry'
-
-module Bio
-  module Velvet
-    class Underground
-      extend FFI::Library
-      ffi_lib File.join(File.dirname(__FILE__),'external','libvelvet.so.1.0')
-
-      class BinarySequenceStore
-        # Parse a CnyUnifiedSeq file in so that sequences can be accessed
-        def initialize(cny_unified_seq_file)
-          readset_pointer = Bio::Velvet::Underground.importCnyReadSet cny_unified_seq_file
-          @readset = Bio::Velvet::Underground::ReadSet.new(readset_pointer)
-        end
-
-        # Return a sequence from the store given its read ID.
-        def [](sequence_id)
-          if sequence_id==0 or sequence_id > @readset[:readCount]
-            raise "Invalid sequence_id #{sequence_id}"
-          end
-
-          pointer = Bio::Velvet::Underground.getTightStringInArray(
-            @readset[:tSequences], sequence_id-1
-            )
-          Bio::Velvet::Underground.readTightString pointer
-        end
-
-        # Number of sequences in this store
-        def length
-          @readset[:readCount]
-        end
-      end
-
-      private
-      # struct readSet_st {
-      #  char **sequences;
-      #  TightString *tSequences;
-      #  char **labels;
-      #  char *tSeqMem;
-      #  Quality **confidenceScores;
-      #  Probability **kmerProbabilities;
-      #  IDnum *mateReads;
-      #  Category *categories;
-      #  unsigned char *secondInPair;
-      #  IDnum readCount;
-      # };
-      class ReadSet < FFI::Struct
-        layout :sequences, :pointer, # char **sequences;
-        :tSequences, :pointer, # TightString *tSequences;
-        :labels, :pointer, # char **labels;
-        :tSeqMem, :pointer, # char *tSeqMem; #TODO: they don't really mean char* here - meant as an unsigned short?
-        :confidenceScores, :pointer, # Quality **confidenceScores;
-        :kmerProbabilities, :pointer, # Probability **kmerProbabilities;
-        :mateReads, :pointer, # IDnum *mateReads;
-        :categories, :pointer, # Category *categories;
-        :secondInPair, :pointer, # unsigned char *secondInPair;
-        :readCount, :int32 # IDnum readCount;
-      end
-
-      # ReadSet *importCnyReadSet(char *filename);
-      attach_function :importCnyReadSet, [:string], :pointer
-
-      # char *readTightString(TightString * tString); #tightString.h
-      attach_function :readTightString, [:pointer], :string
-
-      # TightString *getTightStringInArray(TightString * tString,
-      #			   IDnum	 position);
-      attach_function :getTightStringInArray, [:pointer, :int32], :pointer
-    end
-  end
-end