transrate 1.0.0.beta3 → 1.0.0.beta4

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@@ -17,9 +17,9 @@ class TestOptimiser < Test::Unit::TestCase
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  should "get optimal score" do
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  optimiser = Transrate::ScoreOptimiser.new(@assembly, @readmetrics)
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- assert_in_delta 0.1471, optimiser.raw_score.round(4), 0.005
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+ assert_in_delta 0.1507, optimiser.raw_score.round(4), 0.005
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  optimal, cutoff = optimiser.optimal_score
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- assert_in_delta 0.4252, optimal.round(4), 0.02
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+ assert_in_delta 0.4529, optimal.round(4), 0.05
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  assert_in_delta 0.5638, cutoff.round(4), 0.04
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  end
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@@ -31,17 +31,17 @@ class TestReadMetrics < Test::Unit::TestCase
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  stats = @read_metrics.read_stats
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  assert @read_metrics.has_run, "has run"
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  assert_equal 25006, stats[:fragments], 'number of read pairs'
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- assert_equal 21000, stats[:fragments_mapped], 'number mapping'
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+ assert_in_delta 21744, stats[:fragments_mapped], 10, 'number mapping'
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  assert_in_delta 0.84, stats[:p_fragments_mapped].round(4), 0.05
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  'proportion mapping'
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- assert_in_delta 17382, stats[:good_mappings], 50, 'good mapping'
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- assert_in_delta 0.6945,stats[:p_good_mapping].round(3), 0.005,
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+ assert_in_delta 17983, stats[:good_mappings], 50, 'good mapping'
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+ assert_in_delta 0.719,stats[:p_good_mapping].round(3), 0.005,
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  'percent good mapping'
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- assert_in_delta 3637, stats[:bad_mappings], 50, 'bad mapping'
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- assert_equal 1, stats[:potential_bridges], 'bridges'
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+ assert_in_delta 3761, stats[:bad_mappings], 50, 'bad mapping'
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+ assert_in_delta 2, stats[:potential_bridges], 1, 'bridges'
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  assert_equal 93, stats[:contigs_uncovbase], 'uncovered base contig'
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  assert_equal 28, stats[:contigs_uncovered], 'uncovered contig'
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- assert_equal 72, stats[:contigs_lowcovered], 'lowcovered contig'
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+ assert_equal 71, stats[:contigs_lowcovered], 'lowcovered contig'
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  end
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  end
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  end
@@ -65,7 +65,7 @@ class TestReadMetrics < Test::Unit::TestCase
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  assert_in_delta 0.9364, edit_b.round(4), 0.01, "edit distance 2"
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  assert_in_delta 0.5714, a[:p_good].round(4), 0.01, "prop of good mappings"
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- assert_in_delta 0.8302, b[:p_good].round(4), 0.01, "prop of good mappings"
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+ assert_in_delta 0.8421, b[:p_good].round(4), 0.01, "prop of good mappings"
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  # uncovered bases
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  unc_a = contigs[0].uncovered_bases
@@ -137,9 +137,9 @@ class TestReadMetrics < Test::Unit::TestCase
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  end
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  stats = @read_metrics.read_stats
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  assert @read_metrics.has_run, "has run"
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- assert_equal 1, stats[:potential_bridges], 'bridges'
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+ assert_equal 1, stats[:potential_bridges], "bridges"
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+ assert_in_delta 2, contigs.length, 1, "number of bridging contigs found"
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  assert_equal "Sb01g002430.1", contigs[0].name
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- assert_equal "Sb05g009350.1", contigs[1].name
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  end
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  end
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  end
data/test/test_salmon.rb CHANGED
@@ -19,12 +19,24 @@ class TestSalmon < Test::Unit::TestCase
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  assert_equal 549.279, results['scaffold1'][:tpm], "tpm is wrong"
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  end
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+ should "detect wrong number of columns in the expression file" do
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+ file = File.join(File.dirname(__FILE__), 'data', 'test.sf')
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+ Dir.mktmpdir do |dir|
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+ Dir.chdir dir do
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+ `cut -f1,2,3 #{file} > broken.sf`
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+ assert_raises(Transrate::SalmonError) do
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+ @salmon.load_expression 'broken.sf'
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+ end
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+ end
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+ end
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+ end
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+
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  should "build a command to run salmon" do
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  cmd = @salmon.build_command "assembly.fa", "alignments.bam"
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  cmd = cmd.split(" ")[1..-1].join(" ") # remove command so test is portabl
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  test = "quant --libType IU --alignments alignments.bam "
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  test << "--targets assembly.fa --threads 4 --sampleOut "
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- test << "--sampleUnaligned --output ."
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+ test << "--sampleUnaligned --output . --useVBOpt --useErrorModel"
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  assert_equal test, cmd, "cmd is wrong"
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  end
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@@ -59,7 +59,7 @@ class TestTransrater < Test::Unit::TestCase
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  Dir.chdir tmpdir do
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  all = @rater.all_metrics(@left, @right)
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  score = @rater.assembly_score
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- assert_equal 0.14760, score.round(5) # regression test
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+ assert_equal 0.154, score.round(3) # regression test
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  end
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  end
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  end
data/transrate.gemspec CHANGED
@@ -21,7 +21,7 @@ Gem::Specification.new do |gem|
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  gem.add_dependency 'trollop', '~> 2.0', '>= 2.0.0'
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  gem.add_dependency 'bindeps', '~> 1.1', '>= 1.1.2'
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  gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
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- gem.add_dependency 'crb-blast', '~> 0.5', '>= 0.5.0'
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+ gem.add_dependency 'crb-blast', '~> 0.6', '>= 0.6.4'
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  gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
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  gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: transrate
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  version: !ruby/object:Gem::Version
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- version: 1.0.0.beta3
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+ version: 1.0.0.beta4
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  platform: ruby
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  authors:
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  - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2015-02-23 00:00:00.000000000 Z
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+ date: 2015-06-05 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: yell
@@ -97,20 +97,20 @@ dependencies:
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0.5'
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+ version: '0.6'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 0.5.0
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+ version: 0.6.4
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0.5'
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+ version: '0.6'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 0.5.0
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+ version: 0.6.4
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  - !ruby/object:Gem::Dependency
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  name: fix-trinity-output
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  requirement: !ruby/object:Gem::Requirement
@@ -301,8 +301,6 @@ files:
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  - lib/transrate/salmon.rb
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  - lib/transrate/score_optimiser.rb
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  - lib/transrate/snap.rb
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- - lib/transrate/transrate.bundle
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- - lib/transrate/transrate.so
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  - lib/transrate/transrater.rb
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  - lib/transrate/version.rb
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  - lib/transrate/writer.rb