transrate 0.3.1 → 1.0.0.alpha.1

data/test/test_comp_metrics.rb

@@ -155,36 +155,12 @@ class TestCompMetrics < Test::Unit::TestCase
       @reference["LOC_Os01g11360.1"].seq = "A"*200
       @reference["LOC_Os01g44140.1"].seq = "A"*200
 
+      assert_equal true, crb.target_is_prot, "target is prot"
+      assert_equal false, crb.query_is_prot, "query is prot"
       # total_length of references should be 4400
 
       cov = @comp.coverage crb
-      assert_equal 3600/4400.0, cov, "reference coverage"
-    end
-
-    should "calculate potential chimera count" do
-      crb = @comp.reciprocal_best_blast
-      # # T1   |---------|
-      # # T2                 |---------|
-      # # Q1 |----------------------------| # chimera = true
-
-      crb.remove_hit("scaf_Os10g39590.1")
-      crb.add_hit("scaf_Os10g39590.1", "LOC_Os03g60760.1",
-                     1, 150, 51, 100, 400, 60) # 0.25
-      crb.add_hit("scaf_Os10g39590.1", "LOC_Os10g39590.1",
-                     200, 350, 51, 100, 400, 60) # 0.25
-
-      # # T3   |---------|
-      # # T3                 |---------|
-      # # Q2 |----------------------------|
-      # # chimera = true because the reference has the region 1-100 duplicated
-      crb.remove_hit("scaf_Os12g21920.1")
-      crb.add_hit("scaf_Os12g21920.1", "LOC_Os12g21920.1",
-                     1, 150, 55, 105, 400, 60) # 0.25
-      crb.add_hit("scaf_Os12g21920.1", "LOC_Os12g21920.1",
-                     200, 350, 51, 100, 400, 60) # 0.25
-
-      @comp.chimeras crb
-      assert_equal 2/11.0, @comp.p_chimeras
+      assert_equal 3600/13200.0, cov, "reference coverage"
     end
 
     should "calculate overlap amount" do

data/test/test_contig.rb

@@ -83,6 +83,14 @@ class TestContig < Test::Unit::TestCase
       assert_equal 7, contig.orf_length, "orf length"
     end
 
+    should "get orf length from ATG to stop" do
+      s = "AAATAGATAGATAGAATGAATCAACTAACTAAATAA"
+      # seq = Bio::FastaFormat.new ">test\n#{s}\n>test_r\n#{s.reverse}\n"
+      seq = Bio::FastaFormat.new ">test\n#{s}\n>test_r"
+      contig = Transrate::Contig.new seq
+      assert_equal 6, 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

data/test/test_inline.rb

@@ -18,7 +18,7 @@ class TestInline < Test::Unit::TestCase
         orfs << contig.orf_length
       end
       assert_equal 4, orfs.length
-      assert_equal [333, 370, 131, 84], orfs
+      assert_equal [319, 321, 95, 71], orfs
     end
 
     should 'find longest orf in sequence' do

data/test/test_read_metrics.rb

@@ -8,8 +8,8 @@ class TestReadMetrics < Test::Unit::TestCase
     setup do
       query = File.join(File.dirname(__FILE__), 'data',
                         'sorghum_transcript.fa')
-      assembly = Transrate::Assembly.new(query)
-      @read_metrics = Transrate::ReadMetrics.new(assembly)
+      @assembly = Transrate::Assembly.new(query)
+      @read_metrics = Transrate::ReadMetrics.new(@assembly)
     end
 
     teardown do
@@ -30,30 +30,87 @@ class TestReadMetrics < Test::Unit::TestCase
         Dir.chdir tmpdir do
           @read_metrics.run(left, right)
           stats = @read_metrics.read_stats
-          assert @read_metrics.has_run
-          assert_equal 223, stats[:num_pairs], 'number of read pairs'
-          assert_equal 202, stats[:total_mappings], 'number mapping'
-          assert_equal 90.58, stats[:percent_mapping].round(2),
-                       'percent mapping'
-          assert_equal 202, stats[:good_mappings], 'good mapping'
-          assert_equal 90.58,
-                       stats[:pc_good_mapping].round(2),
+          assert @read_metrics.has_run, "has run"
+          assert_equal 223,     stats[:fragments], 'number of read pairs'
+          assert_equal 217,     stats[:fragments_mapped], 'number mapping'
+          assert_equal 0.9731,   stats[:p_fragments_mapped].round(4),
+                       'proportion mapping'
+          assert_equal 129,     stats[:good_mappings], 'good mapping'
+          assert_equal 0.5785,   stats[:p_good_mapping].round(4),
                        'percent good mapping'
-          assert_equal 0, stats[:bad_mappings], 'bad mapping'
-          assert_equal 22.91, stats[:mean_coverage].round(2), 'mean coverage'
-          assert_equal 11, stats[:n_uncovered_bases], 'n uncovered bases'
-          assert_equal 0.007,
-                       stats[:p_uncovered_bases].round(3),
-                       'p uncovered bases'
+          assert_equal 88,      stats[:bad_mappings], 'bad mapping'
+          assert_equal 2, stats[:potential_bridges], 'bridges'
+          assert_equal 2, stats[:contigs_uncovbase], 'uncovered base contig'
+          assert_equal 0, stats[:contigs_uncovered], 'uncovered contig'
+          assert_equal 0, stats[:contigs_lowcovered], 'lowcovered contig'
+          assert_equal 2, stats[:contigs_good], 'good contigs'
+        end
+      end
+    end
+
+    should "get metrics for individual contigs" do
+      left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
+      right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          @read_metrics.run(left, right)
+          contigs = []
+          @assembly.each do |name, contig|
+            contigs << contig
+          end
+          a = contigs[0].read_metrics
+          b = contigs[1].read_metrics
+
+          edit_a = a[:p_seq_true].round(5)
+          edit_b = b[:p_seq_true].round(5)
+          assert_equal 0.98342, edit_a, "edit distance 1"
+          assert_equal 0.96645, edit_b, "edit distance 2"
+
+          assert_equal 0.59524, a[:p_good].round(5), "proportion of good mappings"
+          assert_equal 0.59398, b[:p_good].round(5), "proportion of good mappings"
+
+          # uncovered bases
+          unc_a = contigs[0].uncovered_bases
+          unc_b = contigs[1].uncovered_bases
+          assert_equal 11, unc_a, "uncovered bases"
+          assert_equal 1, unc_b, "uncovered bases"
+
+          prop_unc_a = a[:p_bases_covered]
+          prop_unc_b = b[:p_bases_covered]
+          assert_equal 0.98497, prop_unc_a.round(5), "proportion covered bases"
+          assert_equal 0.99878, prop_unc_b.round(5), "proportion covered bases"
+
+        end
+      end
+    end
+
+    should "get segmentation probability for individual contigs" do
+      left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
+      right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          @read_metrics.run(left, right)
+          contigs = []
+          @assembly.each do |name, contig|
+            contigs << contig
+          end
+          a = contigs[0].read_metrics
+          b = contigs[1].read_metrics
+
+          edit_a = a[:p_not_segmented].round(5)
+          edit_b = b[:p_not_segmented].round(5)
+          assert_equal 0.11444, edit_a, "probability not segmented 1"
+          assert_equal 0.79629, edit_b, "probability not segmented 2"
+
         end
       end
     end
 
     should "find read pairs that support scaffolding" do
-      left = File.join(File.dirname(__FILE__), 'data', 'bridging_reads.l.fastq')
+      left = File.join(File.dirname(__FILE__),
+                       'data', 'bridging_reads.l.fastq')
       right = File.join(File.dirname(__FILE__),
-                        'data',
-                        'bridging_reads.r.fastq')
+                        'data', 'bridging_reads.r.fastq')
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           @read_metrics.run(left, right)
@@ -63,6 +120,38 @@ class TestReadMetrics < Test::Unit::TestCase
       end
     end
 
+    should "run on a list of input fastq files" do
+      left = []
+      right = []
+      left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
+      right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
+      left << File.join(File.dirname(__FILE__),
+                       'data', 'bridging_reads.l.fastq')
+      right << File.join(File.dirname(__FILE__),
+                        'data', 'bridging_reads.r.fastq')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          @read_metrics.run(left.join(","), right.join(","))
+          stats = @read_metrics.read_stats
+          assert_equal 233, stats[:fragments], 'number of read pairs'
+        end
+      end
+
+    end
+
+    should "calculate read length by scanning fastq files" do
+      left = []
+      right = []
+      left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
+      right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
+      left << File.join(File.dirname(__FILE__),
+                       'data', 'bridging_reads.l.fastq')
+      right << File.join(File.dirname(__FILE__),
+                        'data', 'bridging_reads.r.fastq')
+      @read_metrics.get_read_length(left.join(","), right.join(","))
+      assert_equal 100, @read_metrics.read_length
+    end
+
   end
 
 end

data/test/test_transrater.rb

@@ -8,7 +8,7 @@ class TestTransrater < Test::Unit::TestCase
   context "transrater" do
 
     setup do
-      @assembly = File.join(File.dirname(__FILE__), 'data', 'assembly.2.fa')
+      @assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_transcript.fa')
       @reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
       @rater = Transrate::Transrater.new(@assembly, @reference)
       @left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
@@ -39,8 +39,8 @@ class TestTransrater < Test::Unit::TestCase
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           stats = @rater.assembly_metrics
-          assert_equal 1566, stats.n50
-          assert_equal 10331, stats.n_bases
+          assert_equal 823, stats.n50
+          assert_equal 1555, stats.n_bases
         end
       end
     end
@@ -49,7 +49,7 @@ class TestTransrater < Test::Unit::TestCase
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           stats = @rater.read_metrics(@left, @right)
-          assert_equal 223, stats.read_stats[:num_pairs]
+          assert_equal 223, stats.read_stats[:fragments]
         end
       end
     end
@@ -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 0.55815, score.round(5) # regression test
+          assert_equal 0.40755, score.round(5) # regression test
         end
       end
     end

data/transrate.gemspec

@@ -19,12 +19,9 @@ Gem::Specification.new do |gem|
 
   gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
   gem.add_dependency 'trollop', '~> 2.0'
-  gem.add_dependency 'bindeps', '~> 0.0', '>= 0.0.8'
-  gem.add_dependency 'which', '~> 0.0', '>= 0.0.2'
+  gem.add_dependency 'bindeps', '~> 0.1', '>= 0.1.0'
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
-  gem.add_dependency 'bio-samtools', '~> 2.0', '>= 2.0.5'
-  gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.0'
-  gem.add_dependency 'bettersam', '~> 0.0', '>= 0.0.3'
+  gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.2'
   gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'
 
   gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 1.0.0.alpha.1
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,318 +9,258 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-25 00:00:00.000000000 Z
+date: 2014-10-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.4
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
 - !ruby/object:Gem::Dependency
   name: bindeps
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
-    - - '>='
+        version: '0.1'
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.8
+        version: 0.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
-    - - '>='
+        version: '0.1'
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.8
-- !ruby/object:Gem::Dependency
-  name: which
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '0.0'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.0.2
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '0.0'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.0.2
+        version: 0.1.0
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.3
-- !ruby/object:Gem::Dependency
-  name: bio-samtools
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '2.0'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 2.0.5
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '2.0'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 2.0.5
 - !ruby/object:Gem::Dependency
   name: crb-blast
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.4'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.4'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.4.0
-- !ruby/object:Gem::Dependency
-  name: bettersam
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '0.0'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.3
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '0.0'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.0.3
+        version: 0.4.2
 - !ruby/object:Gem::Dependency
   name: ruby-prof
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.15'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.15.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.15'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.15.1
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 10.3.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
-    - - '>='
+    - - ">="
       - !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
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.7
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.7.5
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.7.5
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.8.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.8.2
 - !ruby/object:Gem::Dependency
   name: shoulda-context
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.1
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
-description: ' a library and command-line tool for quality assessment of de-novo transcriptome
-  assemblies '
+description: " a library and command-line tool for quality assessment of de-novo transcriptome
+  assemblies "
 email: rds45@cam.ac.uk
 executables:
 - transrate
@@ -328,8 +268,8 @@ extensions:
 - ext/transrate/extconf.rb
 extra_rdoc_files: []
 files:
-- .gitignore
-- .travis.yml
+- ".gitignore"
+- ".travis.yml"
 - Gemfile
 - LICENSE
 - README.md
@@ -341,15 +281,14 @@ files:
 - ext/transrate/transrate.c
 - lib/transrate.rb
 - lib/transrate/assembly.rb
-- lib/transrate/bowtie2.rb
 - lib/transrate/cmd.rb
 - lib/transrate/comparative_metrics.rb
 - lib/transrate/contig.rb
 - lib/transrate/contig_metrics.rb
-- lib/transrate/dimension_reduce.rb
-- lib/transrate/metric.rb
+- lib/transrate/express.rb
 - lib/transrate/read_metrics.rb
 - lib/transrate/samtools.rb
+- lib/transrate/snap.rb
 - lib/transrate/transrater.rb
 - lib/transrate/version.rb
 - lib/transrate/writer.rb
@@ -365,7 +304,6 @@ files:
 - test/data/tiny.sam
 - test/helper.rb
 - test/test_bin.rb
-- test/test_bowtie.rb
 - test/test_cmd.rb
 - test/test_comp_metrics.rb
 - test/test_contig.rb
@@ -387,19 +325,18 @@ require_paths:
 - ext
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.4
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: quality assessment of de-novo transcriptome assemblies
 test_files: []
-has_rdoc: