transrate 1.0.0.beta3 → 1.0.0.beta4

data/test/test_optimiser.rb

@@ -17,9 +17,9 @@ class TestOptimiser < Test::Unit::TestCase
 
     should "get optimal score" do
       optimiser = Transrate::ScoreOptimiser.new(@assembly, @readmetrics)
-      assert_in_delta 0.1471, optimiser.raw_score.round(4), 0.005
+      assert_in_delta 0.1507, optimiser.raw_score.round(4), 0.005
       optimal, cutoff = optimiser.optimal_score
-      assert_in_delta 0.4252, optimal.round(4), 0.02
+      assert_in_delta 0.4529, optimal.round(4), 0.05
       assert_in_delta 0.5638, cutoff.round(4), 0.04
     end
 

data/test/test_read_metrics.rb

@@ -31,17 +31,17 @@ class TestReadMetrics < Test::Unit::TestCase
           stats = @read_metrics.read_stats
           assert @read_metrics.has_run, "has run"
           assert_equal 25006,    stats[:fragments], 'number of read pairs'
-          assert_equal 21000,    stats[:fragments_mapped], 'number mapping'
+          assert_in_delta 21744, stats[:fragments_mapped], 10, 'number mapping'
           assert_in_delta 0.84,  stats[:p_fragments_mapped].round(4), 0.05
                        'proportion mapping'
-          assert_in_delta 17382, stats[:good_mappings], 50, 'good mapping'
-          assert_in_delta 0.6945,stats[:p_good_mapping].round(3), 0.005,
+          assert_in_delta 17983, stats[:good_mappings], 50, 'good mapping'
+          assert_in_delta 0.719,stats[:p_good_mapping].round(3), 0.005,
                        'percent good mapping'
-          assert_in_delta 3637,  stats[:bad_mappings], 50, 'bad mapping'
-          assert_equal 1,  stats[:potential_bridges], 'bridges'
+          assert_in_delta 3761,  stats[:bad_mappings], 50, 'bad mapping'
+          assert_in_delta 2,  stats[:potential_bridges], 1, 'bridges'
           assert_equal 93, stats[:contigs_uncovbase], 'uncovered base contig'
           assert_equal 28, stats[:contigs_uncovered], 'uncovered contig'
-          assert_equal 72, stats[:contigs_lowcovered], 'lowcovered contig'
+          assert_equal 71, stats[:contigs_lowcovered], 'lowcovered contig'
         end
       end
     end
@@ -65,7 +65,7 @@ class TestReadMetrics < Test::Unit::TestCase
           assert_in_delta 0.9364, edit_b.round(4), 0.01, "edit distance 2"
 
           assert_in_delta 0.5714, a[:p_good].round(4), 0.01, "prop of good mappings"
-          assert_in_delta 0.8302, b[:p_good].round(4), 0.01, "prop of good mappings"
+          assert_in_delta 0.8421, b[:p_good].round(4), 0.01, "prop of good mappings"
 
           # uncovered bases
           unc_a = contigs[0].uncovered_bases
@@ -137,9 +137,9 @@ class TestReadMetrics < Test::Unit::TestCase
           end
           stats = @read_metrics.read_stats
           assert @read_metrics.has_run, "has run"
-          assert_equal 1,  stats[:potential_bridges], 'bridges'
+          assert_equal 1,  stats[:potential_bridges], "bridges"
+          assert_in_delta 2, contigs.length, 1, "number of bridging contigs found"
           assert_equal "Sb01g002430.1", contigs[0].name
-          assert_equal "Sb05g009350.1", contigs[1].name
         end
       end
     end

data/test/test_salmon.rb

@@ -19,12 +19,24 @@ class TestSalmon < Test::Unit::TestCase
       assert_equal 549.279, results['scaffold1'][:tpm], "tpm is wrong"
     end
 
+    should "detect wrong number of columns in the expression file" do
+      file = File.join(File.dirname(__FILE__), 'data', 'test.sf')
+      Dir.mktmpdir do |dir|
+        Dir.chdir dir do
+          `cut -f1,2,3 #{file} > broken.sf`
+          assert_raises(Transrate::SalmonError) do
+            @salmon.load_expression 'broken.sf'
+          end
+        end
+      end
+    end
+
     should "build a command to run salmon" do
       cmd = @salmon.build_command "assembly.fa", "alignments.bam"
       cmd = cmd.split(" ")[1..-1].join(" ") # remove command so test is portabl
       test = "quant --libType IU --alignments alignments.bam "
       test << "--targets assembly.fa --threads 4 --sampleOut "
-      test << "--sampleUnaligned --output ."
+      test << "--sampleUnaligned --output . --useVBOpt --useErrorModel"
       assert_equal test, cmd, "cmd is wrong"
     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 0.14760, score.round(5) # regression test
+          assert_equal 0.154, score.round(3) # regression test
         end
       end
     end

data/transrate.gemspec

@@ -21,7 +21,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'trollop', '~> 2.0', '>= 2.0.0'
   gem.add_dependency 'bindeps', '~> 1.1', '>= 1.1.2'
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
-  gem.add_dependency 'crb-blast', '~> 0.5', '>= 0.5.0'
+  gem.add_dependency 'crb-blast', '~> 0.6', '>= 0.6.4'
   gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
 
   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: 1.0.0.beta3
+  version: 1.0.0.beta4
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-23 00:00:00.000000000 Z
+date: 2015-06-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -97,20 +97,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.6'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.5.0
+        version: 0.6.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.6'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.5.0
+        version: 0.6.4
 - !ruby/object:Gem::Dependency
   name: fix-trinity-output
   requirement: !ruby/object:Gem::Requirement
@@ -301,8 +301,6 @@ files:
 - lib/transrate/salmon.rb
 - lib/transrate/score_optimiser.rb
 - lib/transrate/snap.rb
-- lib/transrate/transrate.bundle
-- lib/transrate/transrate.so
 - lib/transrate/transrater.rb
 - lib/transrate/version.rb
 - lib/transrate/writer.rb