transrate 1.0.0.beta5 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6010a898aadeb76441e40dc958a2985c3df1d444
-  data.tar.gz: 3c908a057b696e778cb4d369d50798ee8887d271
+  metadata.gz: 1cdc0e54bd5a77cc14727d6c42e739e6c9fa4d10
+  data.tar.gz: ee950d7fcd11d5662a7012c1aeefb597dfe7dd4a
 SHA512:
-  metadata.gz: c9bc4f6e6d390b66a863fb2cd26041f92742738bc4698e2391e8a88e2c712c43d23014461e189ed6646689b87e38231edc5fb728c282d40d6f60e13df4cde864
-  data.tar.gz: cff2caebdb5b477f5675f88550bd1757c1ccb28190d499f303fb24186d69aef88499ca5cfcf0756ff82ef74f3b20c6eeaaac783ae71e049af19fc87641bdf5e1
+  metadata.gz: aa61ac533468fdcd3dbca9949996a4d6c62dcf540fd8f0f7194251b9b88415e28f9c54e884586853ec12244e4778d4bc840a396be3c85c55acb09f71a0d77e4d
+  data.tar.gz: f55918c002f429f1d4912feca88b91e7647bb4064348e254860673d8d9d52bd8bad512b3f7e23e166ad87defbe67de51eeb043620a43dc51eed61e4d40aeece1

data/.gitignore

@@ -67,3 +67,6 @@ traveling-ruby*
 *box
 libruby.so*
 libruby*dylib
+
+# example data
+example_data*

data/Rakefile

@@ -90,7 +90,7 @@ task :default => :test
 # PACKAGING
 
 PACKAGE_NAME = "transrate"
-VERSION = "1.0.0.beta4"
+VERSION = "1.0.0"
 TRAVELING_RUBY_VERSION = "20150210-2.2.0"
 
 desc "Package your app"
@@ -156,10 +156,11 @@ def create_package(target)
   sh "mkdir packaging/bindeps/#{target}/{bin,lib}"
   sh "cd packaging/bindeps/#{target} && " +
      "find . -maxdepth 1 -name '*.tar.gz' -exec tar -xzf '{}' \\; && " +
-     "mv snap bam-read bin/"
+     "mv snap-aligner bam-read bin/ && cp -r ./*/{bin,lib} ."
   sh "cp -r packaging/bindeps/#{target}/{bin,lib} #{package_dir}/"
   # install c extension
-  sh "cp test/vagrant/#{target}/{transrate,libruby}.* #{package_dir}/lib/"
+  sh "cp test/vagrant/#{target}/libruby.* #{package_dir}/lib/"
+  sh "cp test/vagrant/#{target}/transrate.* #{package_dir}/lib/app/ext/transrate/"
   # create package
   if !ENV['DIR_ONLY']
     sh "cd packaging && tar -czf #{package_pref}.tar.gz #{package_pref}"

data/bin/transrate

@@ -173,11 +173,11 @@ else
     end
 
     puts "To install all missing dependencies, run:"
-    puts "  transrate --install-deps"
+    puts "  transrate --install-deps a;;"
     puts "If you only want the read-metrics dependencies:"
-    puts "  transrate --install-read-deps"
+    puts "  transrate --install-deps read"
     puts "Or if you only want the reference-metrics dependencies: "
-    puts "  transrate --install-ref-deps"
+    puts "  transrate --install-deps ref"
 
     exit 1
   end
@@ -290,7 +290,7 @@ assemblies.split(',').each do |assembly|
     pretty_print_hash(contig_results, report_width)
   end
 
-  logger.info "Contig metrics done in #{Time.now - t0} seconds"
+  logger.info "Contig metrics done in #{(Time.now - t0).round} seconds"
 
   read_results = {}
 
@@ -305,7 +305,7 @@ assemblies.split(',').each do |assembly|
       pretty_print_hash(read_results, report_width)
     end
 
-    logger.info "Read metrics done in #{Time.now - t0} seconds"
+    logger.info "Read metrics done in #{(Time.now - t0).round} seconds"
   else
     logger.info "No reads provided, skipping read diagnostics"
   end
@@ -324,7 +324,7 @@ assemblies.split(',').each do |assembly|
       pretty_print_hash(comparative_results, report_width)
     end
 
-    logger.info "Comparative metrics done in #{Time.now - t0} seconds"
+    logger.info "Comparative metrics done in #{(Time.now - t0).round} seconds"
 
     logger.info "-" * report_width
   else
@@ -366,7 +366,7 @@ assemblies.split(',').each do |assembly|
         csv << basic_metrics.keys
         first = false
       end
-      csv << basic_metrics.values
+      csv << basic_metrics.values.map{ |x| x.is_a?(Float) ? x.round(6) : x }
     end
   end
 
@@ -388,6 +388,9 @@ CSV.open(outfile, 'wb') do |file|
   head = [:assembly] + keys
   file << head
   all.each do |row|
-    file << head.map { |x| row[x] }
+    file << head.map { |x|
+      entry = row[x]
+      entry.is_a?(Float) ? entry.round(5) : entry
+    }
   end
 end

data/deps/deps.yaml

@@ -1,23 +1,23 @@
 snap:
   binaries:
-    - snap
+    - snap-aligner
   version:
-    number: '1.0dev.67.trfix1'
-    command: 'snap'
+    number: '1.0beta.18'
+    command: 'snap-aligner'
   url:
     64bit:
-      linux: https://github.com/Blahah/snap/releases/download/v1.0dev.67.trfix1/snap_v1.0dev.67.trfix1_linux.tar.gz
-      macosx: https://github.com/Blahah/snap/releases/download/v1.0dev.67.trfix1/snap_v1.0dev.67.trfix1_macosx.tar.gz
+      linux: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_linux.tar.gz
+      macosx: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_osx.tar.gz
 bam-read:
   binaries:
    - bam-read
   version:
-    number: '1.0.0.beta4'
+    number: '1.0.0'
     command: 'bam-read'
   url:
     64bit:
-      linux: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0.beta4/bam-read_v1.0.0.beta4_linux.tar.gz
-      macosx: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0.beta4/bam-read_v1.0.0.beta4_osx.tar.gz
+      linux: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_linux.tar.gz
+      macosx: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_osx.tar.gz
   unpack: true
 salmon:
   binaries:
@@ -45,5 +45,5 @@ salmon:
     command: 'salmon -v'
   url:
     64bit:
-      linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.0/SalmonBeta-0.4.0_DebianSqueeze.tar.gz
-      macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.0/SalmonBeta-0.4.0_OSX-10.10.tar.gz
+      linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_DebianSqueeze.tar.gz
+      macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_OSX-10.10.tar.gz

data/lib/transrate.rb

@@ -26,6 +26,7 @@ module Transrate
 
 end # Transrate
 
+require 'transrate/transrate'
 require 'transrate/transrater'
 require 'transrate/version'
 require 'transrate/contig'

data/lib/transrate/score_optimiser.rb

@@ -49,7 +49,7 @@ module Transrate
       out = CSV.open("#{prefix}_score_optimisation.csv", 'w')
       out << %w[cutoff assembly_score]
       cutoffscores.each do |c, score|
-        out << [c, score]
+        out << [c.round(5), score.round(5)]
         if score > @optimal
           @optimal = score
           @cutoff = c

data/lib/transrate/snap.rb

@@ -11,7 +11,7 @@ module Transrate
     attr_reader :index_name, :bam, :read_count
 
     def initialize
-      which_snap = Cmd.new('which snap')
+      which_snap = Cmd.new('which snap-aligner')
       which_snap.run
       if !which_snap.status.success?
         raise SnapError.new("could not find snap in the path")

data/lib/transrate/version.rb

@@ -11,7 +11,7 @@ module Transrate
     MAJOR = 1
     MINOR = 0
     PATCH = 0
-    BUILD = 'beta5'
+    BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
   end

data/test/helper.rb

@@ -8,13 +8,14 @@ SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
 SimpleCov.start
 
 require 'minitest/autorun'
-begin; require 'turn/autorun'; rescue LoadError; end
+begin
+  require 'turn/autorun'
+  Turn.config.format = :pretty
+  Turn.config.trace = 5
+rescue LoadError
+end
 require 'shoulda/context'
 require 'transrate'
-require 'transrate/transrate.so'
-
-Turn.config.format = :pretty
-Turn.config.trace = 5
 
 # download large fastq files into test/data/.
 path = "https://github.com/HibberdLab/transrate-test-files/raw/master"
@@ -27,4 +28,4 @@ test_files.each do |file|
     cmd = Transrate::Cmd.new(wget_cmd)
     cmd.run
   end
-end
+end

data/test/test_read_metrics.rb

@@ -31,7 +31,7 @@ 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_in_delta 21744, stats[:fragments_mapped], 10, 'number mapping'
+          assert_in_delta 21732, stats[:fragments_mapped], 10, 'number mapping'
           assert_in_delta 0.84,  stats[:p_fragments_mapped].round(4), 0.05
                        'proportion mapping'
           assert_in_delta 17983, stats[:good_mappings], 50, 'good mapping'
@@ -61,7 +61,7 @@ class TestReadMetrics < Test::Unit::TestCase
 
           edit_a = a[:p_seq_true].round(5)
           edit_b = b[:p_seq_true].round(5)
-          assert_in_delta 0.6597, edit_a.round(4), 0.01, "edit distance 1"
+          assert_in_delta 0.7086, edit_a.round(4), 0.01, "edit distance 1"
           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"

data/transrate.gemspec

@@ -4,7 +4,7 @@ require File.expand_path('../lib/transrate/version', __FILE__)
 
 Gem::Specification.new do |gem|
   gem.name          = 'transrate'
-  gem.authors       = [ "Richard Smith-Unna", "Chris Boursnell" ]
+  gem.authors       = [ "Richard Smith-Unna", "Chris Boursnell", "Rob Patro", "Julian Hibberd", "Steven Kelly" ]
   gem.email         = "rds45@cam.ac.uk"
   gem.licenses      = ["MIT"]
   gem.homepage      = 'https://github.com/Blahah/transrate'
@@ -25,11 +25,12 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
   gem.add_dependency 'colorize', '~> 0.7', '>= 0.7.7'
 
+  gem.add_development_dependency 'test-unit', '~> 3.0'
   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'
-  gem.add_development_dependency 'shoulda-context', '~> 1.2', '>= 1.2.1'
+  gem.add_development_dependency 'shoulda', '~> 3.5', '>= 3.5.0'
   gem.add_development_dependency 'coveralls', '~> 0.7', '>= 0.7.2'
 end

metadata

@@ -1,15 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 1.0.0.beta5
+  version: 1.0.0
 platform: ruby
 authors:
 - Richard Smith-Unna
 - Chris Boursnell
+- Rob Patro
+- Julian Hibberd
+- Steven Kelly
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-11 00:00:00.000000000 Z
+date: 2015-06-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -151,6 +154,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.7.7
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -252,25 +269,25 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 0.8.2
 - !ruby/object:Gem::Dependency
-  name: shoulda-context
+  name: shoulda
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '3.5'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.2.1
+        version: 3.5.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '3.5'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.2.1
+        version: 3.5.0
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
@@ -367,9 +384,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 2.4.6