transrate 0.2.0 → 0.3.0

data/test/test_contig.rb

@@ -1,12 +1,13 @@
 require 'helper'
 require 'bio'
+require 'benchmark'
 
 class TestContig < Test::Unit::TestCase
 
   context "Contig" do
 
     setup do
-      seq = Bio::Sequence.new 'ATGCGTGTATATACGCGTAG'
+      seq = Bio::FastaFormat.new ">test\nATGCGTGTATATACGCGTAG" # cg=3, gc=2, c*g=20
       @contig = Transrate::Contig.new seq
     end
 
@@ -23,6 +24,27 @@ class TestContig < Test::Unit::TestCase
       assert_equal 0.0, @contig.prop_n, "proportion of base n"
     end
 
+    should "calculate dibase composition with ambiguous bases" do
+      seq = Bio::FastaFormat.new ">test\nATGGGNCRYTAG"
+      contig = Transrate::Contig.new seq
+      assert_equal 1, contig.dibase_composition[:at]
+      assert_equal 1, contig.dibase_composition[:nn]
+      assert_equal 1, contig.dibase_composition[:gn]
+    end
+
+    should "benchmark composition" do
+      seq = "GCCGTGAGCTTCTTGATCGAGTTCTTCTCCCGCTTCGCGAACGCCTTGGACTCCTNGCACGGG"
+      seq << "GTCAGCCCCGCGATGTCGGCGGCCGCGGGCGGGGGG"
+      seq = seq * 100000
+      seq = Bio::FastaFormat.new ">test\n"+seq
+      contig = Transrate::Contig.new seq
+      ruby_time = 11 # time taken with the ruby version
+      c_time = Benchmark.realtime do |x|
+        contig.dibase_composition
+      end
+      assert c_time*100 < ruby_time, "c faster than ruby"
+    end
+
     should "know how many of each two-base pair it contains" do
       assert_equal 3, @contig.dibase_composition[:cg], "cg count"
       assert_equal 3, @contig.dibase_composition[:at], "at count"
@@ -36,19 +58,53 @@ class TestContig < Test::Unit::TestCase
     end
 
     should "know its own base-pair skew" do
-      assert_equal 0.45, @contig.gc_skew.round(2), "gc skew"
-      assert_equal 0.55, @contig.at_skew.round(2), "at skew"
+      assert_equal 0.33, @contig.gc_skew.round(2), "gc skew"
+      assert_equal -0.09, @contig.at_skew.round(2), "at skew"
     end
 
-    should "know its own CpG count and density" do
-      assert_equal 3, @contig.cpg_count, "cpg count"
-      assert_equal 66.67, @contig.cpg_ratio.round(2), "cpg ratio"
+    should "know its own CpG count and ratio" do
+      assert_equal 5, @contig.cpg_count, "cpg count"
+      assert_equal 5.56, @contig.cpg_ratio.round(2), "cpg ratio"
+    end
+
+    should "calculate the CpG ratio" do
+      seq = Bio::FastaFormat.new ">test\nAAACGAAA"
+      contig = Transrate::Contig.new seq
+      assert_equal 8, contig.cpg_ratio, "cpg ratio"
     end
 
     should "know the length of its own longest orf" do
       assert_equal 6, @contig.orf_length, "orf length"
     end
 
+    should "not break when there is a null byte in the sequence" do
+      seq = Bio::FastaFormat.new ">test\nAAAAAAAAAAAA\0AAAAAAAAAAA"
+      contig = Transrate::Contig.new seq
+      assert_equal 7, contig.orf_length, "orf length"
+    end
+
+    should "not fail on bases that aren't ACGTN" do
+      seq = Bio::FastaFormat.new ">test\nATGCGTGTARATACGCGTAG"
+      contig = Transrate::Contig.new seq
+      assert_equal 1, contig.base_composition[:n]
+    end
+
+    should "get kmer count with non ACGTN bases" do
+      seq = Bio::FastaFormat.new ">test\nATGCGTGTARATACGCGTAG"
+      contig = Transrate::Contig.new seq
+      assert_equal 0, contig.kmer_count(6, "RRRRRRRRRRRRRRRR")
+    end
+
+    should "calculate linguistic complexity for a long sequence" do
+      alphabet = ["A", "C", "G", "T"]
+      seq = ""
+      50000.times do
+        seq << alphabet.sample
+      end
+      seq = Bio::FastaFormat.new ">test\n"+seq
+      contig = Transrate::Contig.new seq
+      assert contig.linguistic_complexity(6) > 0.98, "linguistic complexity"
+    end
 
     should "know its own linguistic complexity" do
       assert_equal 0.0586, @contig.linguistic_complexity(4).round(4),

data/test/test_contig_metrics.rb

@@ -33,12 +33,12 @@ class TestContigMetrics < Test::Unit::TestCase
 
     should "get CpG density" do
       @contig_metrics.run
-      assert_equal 0.52828, @contig_metrics.cpg_ratio.round(5)
+      assert_equal 1.51939, @contig_metrics.cpg_ratio.round(5)
     end
 
     should "get linguistic complexity" do
       @contig_metrics.run
-      assert_equal 0.26599, @contig_metrics.linguistic_complexity.round(5)
+      assert_equal 0.26526, @contig_metrics.linguistic_complexity.round(5)
     end
 
     should "get the number and proportion of Ns" do

data/test/test_inline.rb

@@ -14,7 +14,7 @@ class TestInline < Test::Unit::TestCase
 
     should 'find longest orf in file' do
       orfs = []
-      @a.assembly.each do |contig|
+      @a.assembly.each_value do |contig|
         orfs << contig.orf_length
       end
       assert_equal 4, orfs.length
@@ -22,7 +22,7 @@ class TestInline < Test::Unit::TestCase
     end
 
     should 'find longest orf in sequence' do
-      seq = Bio::Sequence.new 'ATGCCCCTAGGGTAG'
+      seq = Bio::FastaFormat.new ">test\nATGCCCCTAGGGTAG"
       contig = Transrate::Contig.new seq
       assert_equal 4, contig.orf_length
     end

data/test/test_transrater.rb

@@ -59,7 +59,7 @@ class TestTransrater < Test::Unit::TestCase
         Dir.chdir tmpdir do
           all = @rater.all_metrics(@left, @right)
           score = @rater.assembly_score
-          assert_equal 0.23282, score.round(5)
+          assert_equal 0.55815, score.round(5) # regression test
         end
       end
     end

data/transrate.gemspec

@@ -14,20 +14,21 @@ Gem::Specification.new do |gem|
 
   gem.files = `git ls-files`.split("\n")
   gem.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
-  gem.require_paths = %w( lib )
+  gem.require_paths = %w( lib ext )
+  gem.extensions  = ["ext/transrate/extconf.rb"]
 
   gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
   gem.add_dependency 'trollop', '~> 2.0'
-  gem.add_dependency 'bindeps', '~> 0.0', '>= 0.0.7'
+  gem.add_dependency 'bindeps', '~> 0.0', '>= 0.0.8'
   gem.add_dependency 'which', '~> 0.0', '>= 0.0.2'
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
   gem.add_dependency 'bio-samtools', '~> 2.0', '>= 2.0.5'
-  gem.add_dependency 'RubyInline', '~> 3.12'
-  gem.add_dependency 'crb-blast', '~> 0.2'
+  gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.0'
   gem.add_dependency 'bettersam', '~> 0.0', '>= 0.0.3'
   gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'
 
   gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
+  gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'
   gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'
   gem.add_development_dependency 'minitest', '~> 4', '>= 4.7.5'
   gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-08 00:00:00.000000000 Z
+date: 2014-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -54,7 +54,7 @@ dependencies:
         version: '0.0'
     - - '>='
       - !ruby/object:Gem::Version
-        version: 0.0.7
+        version: 0.0.8
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -64,7 +64,7 @@ dependencies:
         version: '0.0'
     - - '>='
       - !ruby/object:Gem::Version
-        version: 0.0.7
+        version: 0.0.8
 - !ruby/object:Gem::Dependency
   name: which
   requirement: !ruby/object:Gem::Requirement
@@ -125,34 +125,26 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: 2.0.5
-- !ruby/object:Gem::Dependency
-  name: RubyInline
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: crb-blast
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.2'
+        version: '0.4'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.2'
+        version: '0.4'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
 - !ruby/object:Gem::Dependency
   name: bettersam
   requirement: !ruby/object:Gem::Requirement
@@ -213,6 +205,26 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: 10.3.2
+- !ruby/object:Gem::Dependency
+  name: rake-compiler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.9'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.9'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.2
 - !ruby/object:Gem::Dependency
   name: turn
   requirement: !ruby/object:Gem::Requirement
@@ -312,7 +324,8 @@ description: ' a library and command-line tool for quality assessment of de-novo
 email: rds45@cam.ac.uk
 executables:
 - transrate
-extensions: []
+extensions:
+- ext/transrate/extconf.rb
 extra_rdoc_files: []
 files:
 - .gitignore
@@ -323,6 +336,9 @@ files:
 - Rakefile
 - bin/transrate
 - deps/deps.yaml
+- docs/transrate_logo_full.png
+- ext/transrate/extconf.rb
+- ext/transrate/transrate.c
 - lib/transrate.rb
 - lib/transrate/assembly.rb
 - lib/transrate/bowtie2.rb
@@ -348,6 +364,7 @@ files:
 - test/data/sorghum_transcript.fa
 - test/data/tiny.sam
 - test/helper.rb
+- test/test_bin.rb
 - test/test_bowtie.rb
 - test/test_cmd.rb
 - test/test_comp_metrics.rb
@@ -367,6 +384,7 @@ post_install_message:
 rdoc_options: []
 require_paths:
 - lib
+- ext
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - '>='
@@ -379,7 +397,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.6
+rubygems_version: 2.1.4
 signing_key: 
 specification_version: 4
 summary: quality assessment of de-novo transcriptome assemblies