transrate 1.0.0.beta1 → 1.0.0.beta2

data/test/test_bin.rb

@@ -10,27 +10,29 @@ class TestTransrateBin < Test::Unit::TestCase
     end
 
     teardown do
-      files = ["150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.bam.bai",
-      "150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.bam",
-      "sorghum_transcript_into_Os.protein.2.1.blast",
+      files = ["sorghum_100.1.fastq.sorghum_100.2.fastq.sorghum_100.bam.bai",
+      "sorghum_100.1.fastq.sorghum_100.2.fastq.sorghum_100.bam",
+      "sorghum_100_into_Os.protein.2.1.blast",
       "assembly.2_into_Os.protein.2.1.blast",
-      "sorghum_transcript.nhr", "sorghum_transcript.nin", "sorghum_transcript.nsq",
-      "Os.protein.2_into_sorghum_transcript.2.blast",
+      "sorghum_100.nhr", "sorghum_100.nin", "sorghum_100.nsq",
+      "Os.protein.2_into_sorghum_100.2.blast",
       "Os.protein.2_into_assembly.2.2.blast",
       "assembly.2.nhr",  "assembly.2.nin",  "assembly.2.nsq",
       "Os.protein.2.phr",  "Os.protein.2.pin",  "Os.protein.2.psq",
-      "transrate_assemblies.csv", "params.xprs",
-      "sorghum_transcript.fa_results.xprs",
-      "sorghum_transcript.fa_bam_info.csv",
-      "transrate_sorghum_transcript.fa_contigs.csv",
-      "150uncovered.l.fq-150uncovered.r.fq-read_count.txt",
-      "150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.merged.sorted.bam",
-      "bad.sorghum_transcript.fa", "chimeric.sorghum_transcript.fa",
-      "fragmented.sorghum_transcript.fa", "good.sorghum_transcript.fa"]
+      "transrate_assemblies.csv",
+      "sorghum_100.fa_quant.sf",
+      "sorghum_100.fa_bam_info.csv",
+      "transrate_sorghum_100.fa_contigs.csv",
+      "sorghum_100.1.fastq-sorghum_100.2.fastq-read_count.txt",
+      "sorghum_100.1.fastq.sorghum_100.2.fastq.sorghum_100.assigned.bam",
+      "bad.sorghum_100.fa", "chimeric.sorghum_100.fa",
+      "fragmented.sorghum_100.fa", "good.sorghum_100.fa"]
       files.each do |file|
         File.delete(file) if File.exist?(file)
       end
-      `rm -rf sorghum_transcript`
+      `rm -rf sorghum_100`
+      `rm -rf logs`
+      `rm -rf libParams`
     end
 
     should "run help" do
@@ -53,10 +55,10 @@ class TestTransrateBin < Test::Unit::TestCase
     end
 
     should "run on test data" do
-      assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_transcript.fa')
+      assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
       reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
-      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', 'sorghum_100.1.fastq')
+      right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
       cmd = "bundle exec bin/transrate --assembly #{assembly}"
       cmd << " --reference #{reference}"
       cmd << " --left #{left}"
@@ -65,7 +67,7 @@ class TestTransrateBin < Test::Unit::TestCase
       c.run
       assert_equal true, c.status.success?, "exit status"
       assert File.exist?("transrate_assemblies.csv"), "csv file doesn't exist"
-      assert File.exist?("transrate_sorghum_transcript.fa_contigs.csv"),
+      assert File.exist?("transrate_sorghum_100.fa_contigs.csv"),
              "contig csv file doesn't exist"
       hash = {}
       CSV.foreach("transrate_assemblies.csv", :headers => true,
@@ -77,19 +79,20 @@ class TestTransrateBin < Test::Unit::TestCase
           hash[header]=field
         end
       end
-      assert_equal 1555, hash[:n_bases], "number of bases"
-      assert_equal 823, hash[:n50], "n50"
-      assert_equal 0, hash[:n_refs_with_crbb], "number of crb hits"
+      assert_in_delta 137748, hash[:n_bases], 1000, "number of bases"
+      assert_equal 1692, hash[:n50], "n50"
+      assert_equal 2, hash[:n_refs_with_crbb], "number of crb hits"
+      assert_equal 2, hash[:n_contigs_with_crbb], "number of contigs with hits"
     end
 
     should "run on test data with comma separated list of fastq files" do
-      assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_transcript.fa')
+      assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
       left = []
       right = []
+      left << File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
       left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
-      left << File.join(File.dirname(__FILE__), 'data', 'bridging_reads.l.fastq')
+      right << File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
       right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
-      right << File.join(File.dirname(__FILE__), 'data', 'bridging_reads.r.fastq')
       cmd = "bundle exec bin/transrate --assembly #{assembly}"
       cmd << " --left #{left.join(",")}"
       cmd << " --right #{right.join(",")}"
@@ -101,7 +104,7 @@ class TestTransrateBin < Test::Unit::TestCase
       end
       assert_equal true, c.status.success?, "exit status"
       assert File.exist?("transrate_assemblies.csv")
-      assert File.exist?("transrate_sorghum_transcript.fa_contigs.csv"),
+      assert File.exist?("transrate_sorghum_100.fa_contigs.csv"),
              "contig csv file doesn't exist"
       hash = {}
       CSV.foreach("transrate_assemblies.csv", :headers => true,
@@ -111,8 +114,8 @@ class TestTransrateBin < Test::Unit::TestCase
           hash[header]=field
         end
       end
-      assert_equal 1555, hash[:n_bases], "number of bases"
-      assert_equal 823, hash[:n50], "n50"
+      assert_in_delta 137748, hash[:n_bases], 1000, "number of bases"
+      assert_equal 1692, hash[:n50], "n50"
     end
 
     should "fail when one of multiple assemblies is missing" do

data/test/test_cmd.rb

@@ -10,6 +10,11 @@ class TestCmd < Test::Unit::TestCase
       assert_equal "success", cmd.stdout.chomp, 'run echo command'
     end
 
+    should "get the string of a command" do
+      cmd = Transrate::Cmd.new "echo success"
+      assert_equal "echo success", cmd.to_s, 'cmd to string'
+    end
+
   end
 
 end

data/test/test_contig.rb

@@ -7,7 +7,7 @@ class TestContig < Test::Unit::TestCase
   context "Contig" do
 
     setup do
-      seq = Bio::FastaFormat.new ">test\nATGCGTGTATATACGCGTAG" # cg=3, gc=2, c*g=20
+      seq = Bio::FastaFormat.new ">test;\nATGCGTGTATATACGCGTAG" # cg=3, gc=2, c*g=20
       @contig = Transrate::Contig.new seq
     end
 
@@ -32,19 +32,6 @@ class TestContig < Test::Unit::TestCase
       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"
@@ -121,5 +108,13 @@ class TestContig < Test::Unit::TestCase
                    "linguistic complexity k=6"
     end
 
+    should "classify contig" do
+      assert_equal :bad, @contig.classify, "contig is not bad"
+    end
+
+    should "strip trailing semicolons from FASTA entry IDs" do
+      assert_equal "test", @contig.name, "trailing semicolon was not stripped"
+    end
+
   end
 end

data/test/test_read_metrics.rb

@@ -6,15 +6,14 @@ class TestReadMetrics < Test::Unit::TestCase
   context "ReadMetrics" do
 
     setup do
-      query = File.join(File.dirname(__FILE__), 'data',
-                        'sorghum_transcript.fa')
+      query = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
       @assembly = Transrate::Assembly.new(query)
       @read_metrics = Transrate::ReadMetrics.new(@assembly)
     end
 
     teardown do
-      if File.exist?("test/data/sorghum_transcript.fa.fai")
-        rm = "rm test/data/sorghum_transcript.fa.fai"
+      if File.exist?("test/data/sorghum_100.fa.fai")
+        rm = "rm test/data/sorghum_100.fa.fai"
         `#{rm}`
       end
     end
@@ -24,33 +23,33 @@ class TestReadMetrics < Test::Unit::TestCase
     end
 
     should "calculate read mapping statistics" do
-      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', 'sorghum_100.1.fastq')
+      right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           @read_metrics.run(left, right)
           stats = @read_metrics.read_stats
           assert @read_metrics.has_run, "has run"
-          assert_equal 223,     stats[:fragments], 'number of read pairs'
-          assert_equal 215,     stats[:fragments_mapped], 'number mapping'
-          assert_equal 0.9641,   stats[:p_fragments_mapped].round(4),
+          assert_equal 25006,    stats[:fragments], 'number of read pairs'
+          assert_equal 21000,    stats[:fragments_mapped], 'number mapping'
+          assert_in_delta 0.84,  stats[:p_fragments_mapped].round(4), 0.05
                        'proportion mapping'
-          assert_equal 182,     stats[:good_mappings], 'good mapping'
-          assert_equal 0.8161,   stats[:p_good_mapping].round(4),
+          assert_in_delta 17382, stats[:good_mappings], 50, 'good mapping'
+          assert_in_delta 0.6945,stats[:p_good_mapping].round(3), 0.005,
                        'percent good mapping'
-          assert_equal 33,      stats[:bad_mappings], 'bad mapping'
-          assert_equal 1, 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 1, stats[:contigs_good], 'good contigs'
+          assert_in_delta 3637,  stats[:bad_mappings], 50, 'bad mapping'
+          assert_equal 1,  stats[:potential_bridges], '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_in_delta 50, stats[:contigs_good], 10, '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')
+      left = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
+      right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           @read_metrics.run(left, right)
@@ -63,31 +62,49 @@ class TestReadMetrics < Test::Unit::TestCase
 
           edit_a = a[:p_seq_true].round(5)
           edit_b = b[:p_seq_true].round(5)
-          assert_equal 0.98414, edit_a, "edit distance 1"
-          assert_equal 0.974, edit_b, "edit distance 2"
+          assert_in_delta 0.6597, edit_a.round(4), 0.01, "edit distance 1"
+          assert_in_delta 0.9364, edit_b.round(4), 0.01, "edit distance 2"
 
-          assert_equal 0.8046, a[:p_good].round(5),
-                       "proportion of good mappings"
-          assert_equal 0.875, b[:p_good].round(5), "proportion of good mappings"
+          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"
 
           # uncovered bases
           unc_a = contigs[0].uncovered_bases
           unc_b = contigs[1].uncovered_bases
-          assert_equal 11, unc_a, "uncovered bases"
-          assert_equal 3, unc_b, "uncovered bases"
+          assert_in_delta 366, unc_a, 20, "uncovered bases"
+          assert_in_delta 64,  unc_b, 20, "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 0.99635, prop_unc_b.round(5), "proportion covered bases"
+          assert_in_delta 0.5622, prop_unc_a.round(4), 0.05, "proportion covered bases"
+          assert_in_delta 0.9964, prop_unc_b.round(4), 0.05, "proportion covered bases"
 
         end
       end
     end
 
+    should "classify individual contigs" do
+      left = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
+      right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          @read_metrics.run(left, right)
+          contigs = []
+          @assembly.each do |name, contig|
+            contigs << contig
+          end
+          assert_equal :bad,  contigs[0].classify
+          assert_equal :good, contigs[1].classify
+          assert_equal :bad,  contigs[2].classify
+          assert_equal :good, contigs[3].classify
+        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')
+      left = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
+      right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           @read_metrics.run(left, right)
@@ -100,23 +117,30 @@ class TestReadMetrics < Test::Unit::TestCase
 
           edit_a = a[:p_not_segmented].round(5)
           edit_b = b[:p_not_segmented].round(5)
-          assert_equal 0.23527, edit_a, "probability not segmented 1"
-          assert_equal 0.9341, edit_b, "probability not segmented 2"
+          assert_in_delta 0.9965, edit_a.round(4), 0.05, "probability not segmented 1"
+          assert_in_delta 0.9644, edit_b.round(4), 0.05, "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')
-      right = File.join(File.dirname(__FILE__),
-                        'data', 'bridging_reads.r.fastq')
+      left = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
+      right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           @read_metrics.run(left, right)
+          contigs = []
+          @assembly.each do |name, contig|
+            if contig.in_bridges > 0
+              contigs << contig
+            end
+          end
           stats = @read_metrics.read_stats
-          assert_equal 1, stats[:potential_bridges], 'potential bridges'
+          assert @read_metrics.has_run, "has run"
+          assert_equal 1,  stats[:potential_bridges], 'bridges'
+          assert_equal "Sb01g002430.1", contigs[0].name
+          assert_equal "Sb05g009350.1", contigs[1].name
         end
       end
     end
@@ -126,15 +150,15 @@ class TestReadMetrics < Test::Unit::TestCase
       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')
+
+      left << File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
+      right << File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.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'
+          assert_equal 25229, stats[:fragments], 'number of read pairs'
         end
       end
 

data/test/test_salmon.rb

@@ -0,0 +1,33 @@
+require 'helper'
+require 'tmpdir'
+
+class TestSalmon < Test::Unit::TestCase
+
+  context "Salmon" do
+
+    setup do
+      @salmon = Transrate::Salmon.new
+    end
+
+    should "load an expression file" do
+      file = File.join(File.dirname(__FILE__), 'data', 'test.sf')
+      results = @salmon.load_expression file
+      assert_equal 18, results.size, "should be 18 results loaded"
+      assert_equal 1016, results['scaffold1'][:eff_len], "eff length is wrong"
+      assert_equal 20690, results['scaffold1'][:eff_count],
+                   "eff count is wrong"
+      assert_equal 549.279, results['scaffold1'][:tpm], "tpm is wrong"
+    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 ."
+      assert_equal test, cmd, "cmd is wrong"
+    end
+
+  end
+
+end

data/test/test_snap.rb

@@ -0,0 +1,27 @@
+require 'helper'
+require 'tmpdir'
+
+class TestSnap < Test::Unit::TestCase
+
+  context "Snap" do
+
+    setup do
+      @reference = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
+      @left = File.join(File.dirname(__FILE__), "data", "sorghum_100.1.fastq")
+      @right = File.join(File.dirname(__FILE__), "data", "sorghum_100.2.fastq")
+    end
+
+    should "map reads" do
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir(tmpdir) do
+          snap = Transrate::Snap.new
+          snap.build_index(@reference, 4)
+          snap.map_reads(@reference, @left, @right)
+          assert File.exist?(snap.bam), "bam file not found"
+          assert_equal 25006, snap.read_count, "read count"
+        end
+      end
+    end
+
+  end
+end

data/test/test_transrater.rb

@@ -8,11 +8,11 @@ class TestTransrater < Test::Unit::TestCase
   context "transrater" do
 
     setup do
-      @assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_transcript.fa')
+      @assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.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')
-      @right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
+      @left = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
+      @right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
     end
 
     should "create transrater object" do
@@ -20,17 +20,17 @@ class TestTransrater < Test::Unit::TestCase
     end
 
     should "raise error when assembly input is nil" do
-      assert_raise RuntimeError do
+      assert_raise Transrate::TransrateError do
         rater = Transrate::Transrater.new(nil, @reference)
       end
     end
 
-    should "handle assembly as an assemby object" do
+    should "handle assembly as an assembly object" do
       assembly_object = Transrate::Assembly.new(@assembly)
       rater = Transrate::Transrater.new(assembly_object, @reference)
     end
 
-    should "handle reference as an assemby object" do
+    should "handle reference as an assembly object" do
       reference_object = Transrate::Assembly.new(@reference)
       rater = Transrate::Transrater.new(@assembly, reference_object)
     end
@@ -39,8 +39,8 @@ class TestTransrater < Test::Unit::TestCase
       Dir.mktmpdir do |tmpdir|
         Dir.chdir tmpdir do
           stats = @rater.assembly_metrics
-          assert_equal 823, stats.n50
-          assert_equal 1555, stats.n_bases
+          assert_equal 1692, stats.n50
+          assert_equal 137748, 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[:fragments]
+          assert_equal 25006, 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 0.31136, score.round(5) # regression test
+          assert_equal 0.14760, score.round(5) # regression test
         end
       end
     end

data/transrate.gemspec

@@ -19,7 +19,7 @@ Gem::Specification.new do |gem|
 
   gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
   gem.add_dependency 'trollop', '~> 2.0', '>= 2.0.0'
-  gem.add_dependency 'bindeps', '~> 1.0', '>= 1.0.1'
+  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 'ruby-prof', '~> 0.15', '>= 0.15.1'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 1.0.0.beta1
+  version: 1.0.0.beta2
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-08 00:00:00.000000000 Z
+date: 2015-02-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -57,20 +57,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '1.1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: 1.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '1.1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: 1.1.2
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
@@ -302,11 +302,13 @@ extra_rdoc_files: []
 files:
 - ".gitignore"
 - ".travis.yml"
+- CITATION
 - Gemfile
 - LICENSE
 - README.md
 - Rakefile
 - bin/transrate
+- deps/blast.yaml
 - deps/deps.yaml
 - docs/transrate_logo_full.png
 - ext/transrate/extconf.rb
@@ -317,10 +319,8 @@ files:
 - lib/transrate/comparative_metrics.rb
 - lib/transrate/contig.rb
 - lib/transrate/contig_metrics.rb
-- lib/transrate/express.rb
 - lib/transrate/read_metrics.rb
-- lib/transrate/sam_checker.rb
-- lib/transrate/samtools.rb
+- lib/transrate/salmon.rb
 - lib/transrate/score_optimiser.rb
 - lib/transrate/snap.rb
 - lib/transrate/transrater.rb
@@ -334,19 +334,21 @@ files:
 - test/data/assembly.fasta
 - test/data/bridging_reads.l.fastq
 - test/data/bridging_reads.r.fastq
-- test/data/express_results.xprs
+- test/data/sorghum_100.fa
 - test/data/sorghum_transcript.fa
+- test/data/test.sf
 - test/data/tiny.sam
 - test/helper.rb
+- test/test_assembly.rb
 - test/test_bin.rb
 - test/test_cmd.rb
 - test/test_comp_metrics.rb
 - test/test_contig.rb
 - test/test_contig_metrics.rb
-- test/test_express.rb
 - test/test_inline.rb
 - test/test_read_metrics.rb
-- test/test_samtools.rb
+- test/test_salmon.rb
+- test/test_snap.rb
 - test/test_transrate.rb
 - test/test_transrater.rb
 - test/vagrant/centos_6.5_64/Vagrantfile