transrate 1.0.0.beta5 → 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.gitignore +3 -0
- data/Rakefile +4 -3
- data/bin/transrate +11 -8
- data/deps/deps.yaml +10 -10
- data/lib/transrate.rb +1 -0
- data/lib/transrate/score_optimiser.rb +1 -1
- data/lib/transrate/snap.rb +1 -1
- data/lib/transrate/version.rb +1 -1
- data/test/helper.rb +7 -6
- data/test/test_read_metrics.rb +2 -2
- data/transrate.gemspec +3 -2
- metadata +26 -9
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: 1cdc0e54bd5a77cc14727d6c42e739e6c9fa4d10
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4
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data.tar.gz: ee950d7fcd11d5662a7012c1aeefb597dfe7dd4a
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: aa61ac533468fdcd3dbca9949996a4d6c62dcf540fd8f0f7194251b9b88415e28f9c54e884586853ec12244e4778d4bc840a396be3c85c55acb09f71a0d77e4d
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data.tar.gz: f55918c002f429f1d4912feca88b91e7647bb4064348e254860673d8d9d52bd8bad512b3f7e23e166ad87defbe67de51eeb043620a43dc51eed61e4d40aeece1
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data/.gitignore
CHANGED
data/Rakefile
CHANGED
@@ -90,7 +90,7 @@ task :default => :test
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# PACKAGING
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PACKAGE_NAME = "transrate"
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VERSION = "1.0.0
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VERSION = "1.0.0"
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TRAVELING_RUBY_VERSION = "20150210-2.2.0"
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desc "Package your app"
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@@ -156,10 +156,11 @@ def create_package(target)
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sh "mkdir packaging/bindeps/#{target}/{bin,lib}"
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sh "cd packaging/bindeps/#{target} && " +
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"find . -maxdepth 1 -name '*.tar.gz' -exec tar -xzf '{}' \\; && " +
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-
"mv snap bam-read bin/"
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"mv snap-aligner bam-read bin/ && cp -r ./*/{bin,lib} ."
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sh "cp -r packaging/bindeps/#{target}/{bin,lib} #{package_dir}/"
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# install c extension
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sh "cp test/vagrant/#{target}/
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sh "cp test/vagrant/#{target}/libruby.* #{package_dir}/lib/"
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sh "cp test/vagrant/#{target}/transrate.* #{package_dir}/lib/app/ext/transrate/"
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# create package
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if !ENV['DIR_ONLY']
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sh "cd packaging && tar -czf #{package_pref}.tar.gz #{package_pref}"
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data/bin/transrate
CHANGED
@@ -173,11 +173,11 @@ else
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end
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puts "To install all missing dependencies, run:"
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puts " transrate --install-deps"
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puts " transrate --install-deps a;;"
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puts "If you only want the read-metrics dependencies:"
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puts " transrate --install-read
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puts " transrate --install-deps read"
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puts "Or if you only want the reference-metrics dependencies: "
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puts " transrate --install-ref
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puts " transrate --install-deps ref"
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exit 1
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end
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@@ -290,7 +290,7 @@ assemblies.split(',').each do |assembly|
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pretty_print_hash(contig_results, report_width)
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end
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logger.info "Contig metrics done in #{Time.now - t0} seconds"
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logger.info "Contig metrics done in #{(Time.now - t0).round} seconds"
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read_results = {}
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@@ -305,7 +305,7 @@ assemblies.split(',').each do |assembly|
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pretty_print_hash(read_results, report_width)
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end
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logger.info "Read metrics done in #{Time.now - t0} seconds"
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logger.info "Read metrics done in #{(Time.now - t0).round} seconds"
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else
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logger.info "No reads provided, skipping read diagnostics"
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end
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@@ -324,7 +324,7 @@ assemblies.split(',').each do |assembly|
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pretty_print_hash(comparative_results, report_width)
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end
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logger.info "Comparative metrics done in #{Time.now - t0} seconds"
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logger.info "Comparative metrics done in #{(Time.now - t0).round} seconds"
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logger.info "-" * report_width
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else
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@@ -366,7 +366,7 @@ assemblies.split(',').each do |assembly|
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csv << basic_metrics.keys
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first = false
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end
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csv << basic_metrics.values
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csv << basic_metrics.values.map{ |x| x.is_a?(Float) ? x.round(6) : x }
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end
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end
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@@ -388,6 +388,9 @@ CSV.open(outfile, 'wb') do |file|
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head = [:assembly] + keys
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file << head
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all.each do |row|
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file << head.map { |x|
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file << head.map { |x|
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entry = row[x]
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entry.is_a?(Float) ? entry.round(5) : entry
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}
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end
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end
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data/deps/deps.yaml
CHANGED
@@ -1,23 +1,23 @@
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snap:
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binaries:
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- snap
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- snap-aligner
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version:
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number: '1.
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command: 'snap'
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number: '1.0beta.18'
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command: 'snap-aligner'
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url:
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64bit:
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linux: https://github.com/Blahah/snap/releases/download/v1.
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macosx: https://github.com/Blahah/snap/releases/download/v1.
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linux: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_linux.tar.gz
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macosx: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_osx.tar.gz
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bam-read:
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binaries:
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- bam-read
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version:
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number: '1.0.0
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number: '1.0.0'
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command: 'bam-read'
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url:
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64bit:
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linux: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0
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macosx: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0
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linux: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_linux.tar.gz
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macosx: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_osx.tar.gz
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unpack: true
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salmon:
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binaries:
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@@ -45,5 +45,5 @@ salmon:
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command: 'salmon -v'
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url:
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64bit:
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linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.
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macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.
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linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_DebianSqueeze.tar.gz
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macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_OSX-10.10.tar.gz
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data/lib/transrate.rb
CHANGED
@@ -49,7 +49,7 @@ module Transrate
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out = CSV.open("#{prefix}_score_optimisation.csv", 'w')
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out << %w[cutoff assembly_score]
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cutoffscores.each do |c, score|
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out << [c, score]
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out << [c.round(5), score.round(5)]
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if score > @optimal
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@optimal = score
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@cutoff = c
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data/lib/transrate/snap.rb
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@@ -11,7 +11,7 @@ module Transrate
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attr_reader :index_name, :bam, :read_count
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def initialize
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which_snap = Cmd.new('which snap')
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which_snap = Cmd.new('which snap-aligner')
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which_snap.run
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if !which_snap.status.success?
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raise SnapError.new("could not find snap in the path")
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data/lib/transrate/version.rb
CHANGED
data/test/helper.rb
CHANGED
@@ -8,13 +8,14 @@ SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
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SimpleCov.start
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require 'minitest/autorun'
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begin
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begin
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require 'turn/autorun'
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Turn.config.format = :pretty
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Turn.config.trace = 5
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rescue LoadError
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end
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require 'shoulda/context'
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require 'transrate'
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require 'transrate/transrate.so'
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Turn.config.format = :pretty
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Turn.config.trace = 5
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# download large fastq files into test/data/.
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path = "https://github.com/HibberdLab/transrate-test-files/raw/master"
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cmd = Transrate::Cmd.new(wget_cmd)
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cmd.run
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end
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end
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end
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data/test/test_read_metrics.rb
CHANGED
@@ -31,7 +31,7 @@ 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_in_delta
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assert_in_delta 21732, 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 17983, stats[:good_mappings], 50, 'good mapping'
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edit_a = a[:p_seq_true].round(5)
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edit_b = b[:p_seq_true].round(5)
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assert_in_delta 0.
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assert_in_delta 0.7086, edit_a.round(4), 0.01, "edit distance 1"
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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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data/transrate.gemspec
CHANGED
@@ -4,7 +4,7 @@ require File.expand_path('../lib/transrate/version', __FILE__)
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Gem::Specification.new do |gem|
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gem.name = 'transrate'
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gem.authors = [ "Richard Smith-Unna", "Chris Boursnell" ]
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gem.authors = [ "Richard Smith-Unna", "Chris Boursnell", "Rob Patro", "Julian Hibberd", "Steven Kelly" ]
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gem.email = "rds45@cam.ac.uk"
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gem.licenses = ["MIT"]
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gem.homepage = 'https://github.com/Blahah/transrate'
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@@ -25,11 +25,12 @@ Gem::Specification.new do |gem|
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gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
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gem.add_dependency 'colorize', '~> 0.7', '>= 0.7.7'
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gem.add_development_dependency 'test-unit', '~> 3.0'
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gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
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gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'
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gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'
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gem.add_development_dependency 'minitest', '~> 4', '>= 4.7.5'
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gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2'
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gem.add_development_dependency 'shoulda
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gem.add_development_dependency 'shoulda', '~> 3.5', '>= 3.5.0'
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gem.add_development_dependency 'coveralls', '~> 0.7', '>= 0.7.2'
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end
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metadata
CHANGED
@@ -1,15 +1,18 @@
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1
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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
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version: 1.0.0
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platform: ruby
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authors:
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- Richard Smith-Unna
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- Chris Boursnell
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- Rob Patro
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- Julian Hibberd
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- Steven Kelly
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2015-06-
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date: 2015-06-15 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: yell
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@@ -151,6 +154,20 @@ dependencies:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.7.7
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- !ruby/object:Gem::Dependency
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name: test-unit
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requirement: !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: '3.0'
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type: :development
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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: '3.0'
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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@@ -252,25 +269,25 @@ dependencies:
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- !ruby/object:Gem::Version
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version: 0.8.2
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- !ruby/object:Gem::Dependency
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name: shoulda
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name: shoulda
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requirement: !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: '
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version: '3.5'
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- - ">="
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- !ruby/object:Gem::Version
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version:
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version: 3.5.0
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type: :development
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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: '
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version: '3.5'
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- - ">="
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- !ruby/object:Gem::Version
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version:
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version: 3.5.0
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- !ruby/object:Gem::Dependency
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name: coveralls
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requirement: !ruby/object:Gem::Requirement
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@@ -367,9 +384,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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-
- - "
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+
- - ">="
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- !ruby/object:Gem::Version
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version:
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.4.6
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