transrate 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+coverage
+InstalledFiles
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+
+# YARD artifacts
+.yardoc
+_yardoc
+doc/

data/Gemfile

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+source "https://rubygems.org"
+
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    transrate (0.0.1)
+      bettersam
+      bio
+      rake (~> 10.1.0)
+      trollop (~> 2.0)
+      which
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ansi (1.4.3)
+    bettersam (0.0.1.alpha)
+    bio (1.4.3)
+    colorize (0.5.8)
+    coveralls (0.6.7)
+      colorize
+      multi_json (~> 1.3)
+      rest-client
+      simplecov (>= 0.7)
+      thor
+    facade (1.0.5)
+    mime-types (1.23)
+    multi_json (1.7.7)
+    pathname2 (1.6.5)
+      facade
+    rake (10.1.0)
+    rest-client (1.6.7)
+      mime-types (>= 1.16)
+    shoulda-context (1.1.5)
+    simplecov (0.7.1)
+      multi_json (~> 1.0)
+      simplecov-html (~> 0.7.1)
+    simplecov-html (0.7.1)
+    thor (0.16.0)
+    trollop (2.0)
+    turn (0.9.6)
+      ansi
+    which (0.0.2)
+      pathname2 (>= 1.4.4)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  coveralls (~> 0.6.7)
+  shoulda-context
+  simplecov
+  transrate!
+  turn

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2013 Richard Smith
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+Transrate
+----
+
+Quality analyis and comparison of transcriptome assemblies.
+
+
+## Installation
+
+You can install transrate very easily. Just run at the terminal:
+
+`gem install transrate`
+
+If that doesn't work, check the requirements below...
+
+## Usage
+
+
+## Requirements
+
+### Ruby
+
+First, you'll need Ruby v1.9.3 or greater installed. You can check with:
+
+`ruby --version`
+
+If you don't have Ruby installed, or you need a higher version, I recommend using [RVM](http://rvm.io/) as your Ruby Version Manager. To install RVM along with the latest ruby, just run:
+
+`\curl -L https://get.rvm.io | bash -s stable`
+
+### Rubygems
+
+Your Ruby installation *should* come with RubyGems, the package manager for Ruby. You can check with:
+
+`gem --version`
+
+If you don't have it installed, I recommend installing the latest version of Ruby and RubyGems using the RVM instructions above (in the Requirements:Ruby section.
+
+## Development status
+
+This software is in very early development. Nevertheless, we welcome bug reports.

data/bin/transrate

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+#!/usr/bin/env ruby
+
+require 'trollop'
+require 'transrate'
+
+opts = Trollop::options do
+  version "v0.0.1a"
+  banner <<-EOS
+
+Transrate v0.0.1a by Richard Smith <rds45@cam.ac.uk>
+
+DESCRIPTION:
+Analyse a de-novo transcriptome
+assembly using three kinds of metrics:
+
+1. contig-based
+2. read-mapping
+3. reference-based
+
+Please make sure USEARCH and bowtie2 are both installed
+and in the PATH.
+
+Bug reports and feature requests at:
+http://github.com/blahah/transrate
+
+USAGE:
+transrate <options>
+
+OPTIONS:
+
+EOS
+  opt :assembly, "assembly file in FASTA format", :required => true, :type => String
+  opt :reference, "reference proteome file in FASTA format", :required => true, :type => String
+  opt :left, "left reads file in FASTQ format", :type => String
+  opt :right, "right reads file in FASTQ format", :type => String
+  opt :insertsize, "mean insert size",  :default => 200, :type => Integer
+  opt :insertsd, "insert size standard deviation", :default => 50, :type => Integer
+  opt :threads, "number of threads to use", :default => 8, :type => Integer
+end
+
+def pretty_print_hash hash, width
+  hash.map{ |k, v| "#{k.to_s}#{" " * (width - (k.length + v.to_i.to_s.length))}#{v.to_i}" }.join("\n")
+end
+
+include Transrate
+
+a = Assembly.new opts.assembly
+r = Assembly.new opts.reference
+
+puts "\n\nAnalysing assembly: #{opts.assembly}\n\n"
+
+puts "calculating contig stats..."
+t0 = Time.now
+contig_results = a.basic_stats
+puts "...done in #{Time.now - t0} seconds"
+
+read_results = nil
+if (opts.left && opts.right)
+  puts "\ncalculating read diagnostics..."
+  t0 = Time.now
+  read_metrics = ReadMetrics.new a
+  read_results = read_metrics.run(opts.left, opts.right)
+  puts "...done in #{Time.now - t0} seconds"
+else
+  puts "\nno reads provided, skipping read diagnostics"
+end
+
+puts "\ncalculating comparative metrics..."
+t0 = Time.now
+comparative_metrics = ComparativeMetrics.new(a, r)
+comparative_results = comparative_metrics.run
+puts "...done in #{Time.now - t0} seconds"
+
+report_width = 30
+
+if contig_results
+  puts "\n\n"
+  puts "Contig metrics:"
+  puts "-" *  report_width
+  puts pretty_print_hash(contig_results, report_width)
+end
+
+if read_results
+  puts "\n\n"
+  puts "Read mapping metrics:"
+  puts "-" *  report_width
+  puts pretty_print_hash(read_results, report_width)
+end
+
+if comparative_results
+  puts "\n\n"
+  puts "Comparative metrics:"
+  puts "-" *  report_width
+  puts pretty_print_hash(comparative_results, report_width)
+end

data/lib/transrate.rb

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+require 'transrate/version'
+require 'transrate/assembly'
+require 'transrate/bowtie2'
+require 'transrate/read_metrics'
+require 'transrate/usearch'
+require 'transrate/rb_hit'
+require 'transrate/reciprocal_annotation'
+require 'transrate/comparative_metrics'

data/lib/transrate/assembly.rb

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+require 'bio'
+require 'bettersam'
+require 'csv'
+require 'forwardable'
+
+class Assembly
+
+  include Enumerable
+  extend Forwardable
+  def_delegators :@assembly, :each, :<<
+
+  attr_accessor :ublast_db
+  attr_accessor :orfs_ublast_db
+  attr_accessor :protein
+
+  # number of bases in the assembly
+  attr_writer :n_bases
+
+  # assembly filename
+  attr_accessor :file
+
+  # Reuturn a new Assembly.
+  #
+  # - +:assembly+ - an array of Bio::Sequences
+  def initialize file
+    @file = file
+    @assembly = []
+    @n_bases = 0
+    Bio::FastaFormat.open(file).each do |entry|
+      @n_bases += entry.length
+      @assembly << entry
+    end
+    @assembly.sort_by! { |x| x.length }
+  end
+
+  # Return a new Assembly object by loading sequences
+  # from the FASTA-format +:file+
+  def self.stats_from_fasta file
+    a = Assembly.new file
+    a.basic_stats
+  end
+
+  # Return a hash of statistics about this assembly
+  def basic_stats
+    cumulative_length = 0.0
+    # we'll calculate Nx for all these x
+    x = [90, 70, 50, 30, 10]
+    x2 = x.clone
+    cutoff = x2.pop / 100.0
+    res = []
+    n1k = 0
+    n10k = 0
+    @assembly.each do |s|
+      new_cum_len = cumulative_length + s.length
+      prop = new_cum_len / self.n_bases
+      n1k += 1 if s.length > 1_000
+      n10k += 1 if s.length > 10_000
+      if prop >= cutoff
+        res << s.length
+        break if x2.empty?
+        cutoff = x2.pop / 100.0
+      end
+      cumulative_length = new_cum_len
+    end
+    mean = cumulative_length / @assembly.size
+    ns = Hash[x.map { |n| "N#{n}" }.zip(res)]
+    {
+      "n_seqs" => @assembly.size,
+      "smallest" => @assembly.first.length,
+      "largest" => @assembly.last.length,
+      "n_bases" => @n_bases,
+      "mean_len" => mean,
+      "n > 1k" => n1k,
+      "n > 10k" => n10k
+    }.merge ns
+  end
+
+  # return the number of bases in the assembly, calculating
+  # from the assembly if it hasn't already been done.
+  def n_bases
+    unless @n_bases
+      @n_bases = 0
+      @assembly.each { |s| @n_bases += s.length }
+    end
+    @n_bases
+  end
+
+  def print_stats
+    self.basic_stats.map do |k, v| 
+      "#{k}#{" " * (20 - (k.length + v.to_i.to_s.length))}#{v.to_i}"
+    end.join("\n")
+  end
+
+end # Assembly

data/lib/transrate/bowtie2.rb

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+module Transrate
+
+  class Bowtie2
+
+    require 'which'
+    include Which
+
+    def initialize
+      bowtie2_path = which('bowtie2')
+      raise "could not find bowtie2 in the path" if bowtie2_path.empty?
+      @bowtie2 = bowtie2_path.first
+      bowtie2_build_path = which('bowtie2-build')
+      raise "could not find bowtie2-build in the path" if bowtie2_build_path.empty?
+      @bowtie2_build = bowtie2_build_path.first
+    end
+
+    def map_reads file, left, right=nil, insertsize=200, insertsd=50, outputname=nil
+      lbase = File.basename(left)
+      rbase = File.basename(right)
+      outputname ||= "#{lbase}.#{rbase}.sam"
+      realistic_dist = insertsize + (3 * insertsd)
+      unless File.exists? outputname
+        # construct bowtie command
+        bowtiecmd = "#{@bowtie2} -k 3 -p 8 -X #{realistic_dist}"
+        bowtiecmd += " --no-unal --local --quiet"
+        bowtiecmd += " #{File.basename(file)} -1 #{left}"
+        # paired end?
+        bowtiecmd += " -2 #{right}" if right
+        bowtiecmd += " > #{outputname}"
+        # run bowtie
+        `#{bowtiecmd}`
+      end
+      outputname
+    end
+
+    def build_index file
+      unless File.exists?(file + '.1.bt2')
+        `#{@bowtie2_build} --offrate 1 #{file} #{File.basename(file)}`
+      end
+    end
+
+  end # Bowtie2
+
+end # Transrate

data/lib/transrate/comparative_metrics.rb

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+require 'set'
+
+module Transrate
+  
+  class ComparativeMetrics
+
+    def initialize assembly, reference
+      @assembly = assembly
+      @reference = reference
+      @usearch = Usearch.new
+    end
+
+    def run
+      rbu = self.reciprocal_best_ublast
+      ohr = self.ortholog_hit_ratio rbu
+      cf = self.collapse_factor @ra.l2r_hits
+      {
+        :reciprocal_hits => rbu.size,
+        :ortholog_hit_ratio => ohr,
+        :collapse_factor => cf
+      }
+    end
+
+    def reciprocal_best_ublast
+      @ra = ReciprocalAnnotation.new @assembly, @reference
+      @ra.run
+    end
+
+    def ortholog_hit_ratio rbu
+      rbu.reduce(0.0){ |sum, hit| sum += hit.last.tcov.to_f } / rbu.size
+    end
+
+    def collapse_factor hits
+      targets = {}
+      hits.each_pair do |query, hit|
+        unless targets.has_key? query
+          targets[query] = Set.new
+        end
+        targets[query] << hit.target
+      end
+      targets.values.reduce(0.0){ |sum, val| sum += val.size } / targets.size
+    end
+
+  end # ComparativeMetrics
+
+end # Transrate

data/lib/transrate/rb_hit.rb

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+module Transrate
+
+  class RBHit
+
+    # Fields: query id, subject id, % identity, alignment length, mismatches,
+    # gap opens, q. start, q. end, s. start, s. end, evalue, bit score
+    attr_accessor :query, :target, :id, :alnlen, :mismatches
+    attr_accessor :gaps, :qstart, :qend, :tstart, :tend, :evalue
+    attr_accessor :bitscore, :tcov
+    
+    def initialize(list)
+      @query      = list[0].scan(/[^|]+/).first.split.first # extract only identifier
+      @target     = list[1].scan(/[^|]+/).first.split.first
+      @id         = list[2]
+      @alnlen     = list[3]
+      @mismatches = list[4]
+      @gaps       = list[5]
+      @qstart     = list[6]
+      @qend       = list[7]
+      @tstart     = list[8]
+      @tend       = list[9]
+      @evalue     = list[10]
+      @bitscore   = list[11]
+      @tcov       = list[12]
+    end
+
+    def to_s
+      @query + " => " + @target
+    end
+
+  end # RBHit
+
+end # Transrate

data/lib/transrate/read_metrics.rb

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+module Transrate
+
+  class ReadMetrics
+
+    def initialize assembly
+      @assembly = assembly
+      @mapper = Bowtie2.new
+      self.initial_values
+    end
+
+    def run left, right, insertsize=200, insertsd=50
+      @mapper.build_index @assembly.file
+      samfile = @mapper.map_reads(@assembly.file, 
+                                  left, right, 
+                                  insertsize, insertsd)
+      self.analyse_read_mappings(samfile, insertsize, insertsd)
+      {
+        :total_mappings => @total,
+        :good_mappings => @good,
+        :bad_mappings => @bad,
+        :both_mapped => @both_mapped,
+        :properly_paired => @properly_paired,
+        :improper_paired => @improperly_paired,
+        :proper_orientation => @proper_orientation,
+        :improper_orientation => @improper_orientation,
+        :same_contig => @same_contig,
+        :realistic_overlap => @realistic_overlap,
+        :unrealistic_overlap => @unrealistic_overlap,
+        :realistic_fragment => @realistic_fragment,
+        :unrealistic_fragment => @unrealistic_fragment,
+        :potential_bridges => @supported_bridges
+      }
+    end
+
+    def analyse_read_mappings samfile, insertsize, insertsd, bridge=true
+      @bridges = {} if bridge
+      realistic_dist = self.realistic_distance(insertsize, insertsd)
+      if File.exists?(samfile) && File.size(samfile) > 0
+        ls = BetterSam.new
+        rs = BetterSam.new
+        sam = File.open(samfile).each_line
+        sam.each_slice(2) do |l, r|
+          if (l && r) && (ls.parse_line(l) && rs.parse_line(r))
+            self.check_read_pair(ls, rs, realistic_dist)
+          end
+        end
+        self.check_bridges if bridge
+      else
+        raise "samfile #{samfile} not found"
+      end
+    end
+
+    def initial_values
+      @total = 0
+      @good = 0
+      @bad = 0
+      @both_mapped = 0
+      @properly_paired = 0
+      @improperly_paired = 0
+      @proper_orientation = 0
+      @improper_orientation = 0
+      @same_contig = 0
+      @realistic_overlap = 0
+      @unrealistic_overlap = 0
+      @realistic_fragment = 0
+      @unrealistic_fragment = 0
+    end
+
+    def realistic_distance insertsize, insertsd
+      insertsize + (3 * insertsd)
+    end
+
+    def check_read_pair ls, rs, realistic_dist
+      return unless ls.primary_aln?
+      @total += 1
+      if ls.both_mapped?
+        # reads are paired
+        @both_mapped += 1
+        if ls.read_properly_paired?
+          # mapped in proper pair
+          @properly_paired += 1
+          self.check_orientation(ls, rs)
+        else
+          # not mapped in proper pair
+          @improperly_paired += 1
+          if ls.chrom == rs.chrom
+            # both on same contig
+            @same_contig += 1
+            self.check_overlap_plausibility(ls, rs)
+          else
+            self.check_fragment_plausibility(ls, rs, realistic_dist)
+          end
+        end
+      end
+    end
+
+    def check_orientation ls, rs
+      if ls.pair_opposite_strands?
+        # mates in proper orientation
+        @proper_orientation += 1
+        @good += 1
+      else
+        # mates in wrong orientation
+        @improper_orientation += 1
+        @bad += 1
+      end
+    end
+
+    def check_overlap_plausibility ls, rs
+      if Math.sqrt((ls.pos - rs.pos) ** 2) < ls.seq.length
+        # overlap is realistic
+        @realistic_overlap += 1
+        self.check_orientation(ls, rs)
+      else
+        # overlap not realistic
+        @unrealistic_overlap+= 1
+        @bad += 1
+      end
+    end
+
+    def check_fragment_plausibility ls, rs, realistic_dist
+      # mates on different contigs
+      # are the mapping positions within a realistic distance of
+      # the ends of contigs?
+      ldist = [ls.pos, ls.seq.length - ls.pos].min
+      rdist = [rs.pos, rs.seq.length - rs.pos].min
+      if ldist + rdist <= realistic_dist
+        # increase the evidence for this bridge
+        key = [ls.chrom, rs.chrom].sort.join("<>").to_sym
+        if @bridges.has_key? key
+          @bridges[key] += 1
+        else
+          @bridges[key] = 1
+        end
+        @realistic_fragment += 1
+        @good += 1
+      else
+        @unrealistic_fragment += 1
+        @bad += 1
+      end
+    end
+
+    def check_bridges
+      @supported_bridges = 0
+      CSV.open('supported_bridges.csv', 'w') do |f|
+        @bridges.each_pair do |b, count|
+          start, finish = b.to_s.split('<>')
+          if count > 1
+            f << [start, finish, count]
+            @supported_bridges += 1
+          end
+        end
+      end
+    end
+
+  end # ReadMetrics
+
+end # Transrate

data/lib/transrate/reciprocal_annotation.rb

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+module Transrate
+
+  class ReciprocalAnnotation
+
+    attr_reader :l2r_hits
+    attr_reader :r2l_hits
+    attr_reader :results
+
+    def initialize assembly, reference
+      @assembly = assembly
+      @reference = reference
+      @usearch = Usearch.new
+    end
+
+    def run
+      self.make_assembly_db
+      self.make_reference_db
+      left2right, right2left = self.reciprocal_align
+      self.parse_results left2right, right2left
+      @results
+    end
+
+    def make_assembly_db
+      unless @assembly.orfs_ublast_db
+        assembly_base = File.basename(@assembly.file, ".*")
+        assembly_orfs = assembly_base + ".orfs"
+        @usearch.findorfs @assembly.file, assembly_orfs
+        assembly_db = assembly_base + ".udb"
+        @usearch.makeudb_ublast assembly_orfs, assembly_db
+        @assembly.orfs_ublast_db = assembly_db
+      end
+    end
+
+    def make_reference_db
+      unless @reference.ublast_db
+        reference_base = File.basename(@reference.file, ".*")
+        reference_db = reference_base + ".udb"
+        @usearch.makeudb_ublast @reference.file, reference_db
+        @reference.ublast_db = reference_db
+      end
+    end
+
+    def reciprocal_align
+      left2right = @usearch.ublast @assembly.file, @reference.ublast_db
+      right2left = @usearch.ublast @reference.file, @assembly.orfs_ublast_db
+      [left2right, right2left]
+    end
+
+    def parse_results left2right, right2left
+      l2r_results = self.load_results_file left2right
+      r2l_results = self.load_results_file right2left
+      @l2r_hits = self.results_to_hits l2r_results
+      @r2l_hits = self.results_to_hits r2l_results
+      @results = {}
+      @l2r_hits.each_pair do |query, best|
+        next if best.nil?
+        tbest = @r2l_hits[best.target]
+        next if tbest.nil?
+        @results[query] = best if query == tbest.target
+      end
+    end
+
+    def results_to_hits results
+      hits = {}
+      results.each do |hit|
+        if hits.has_key? hit.query
+          old_hit = hits[hit.query]
+          old_eval, old_bits = old_hit.evalue, old_hit.bitscore
+          if hit.bitscore > old_bits
+            hits[hit.query] = hit 
+          elsif hit.bitscore == old_bits && hit.evalue < old_eval
+            hits[hit.query] = hit
+          end
+        else
+          hits[hit.query] = hit
+        end
+      end
+      hits
+    end
+
+    def load_results_file file
+      results = []
+      File.open(file).each_line do |line|
+        results << RBHit.new(line.chomp.split("\t"))
+      end
+      results
+    end
+
+  end # ReciprocalAnnotation
+
+end # Transrate

data/lib/transrate/usearch.rb

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+module Transrate
+
+  class Usearch
+
+    require 'which'
+    include Which
+
+    def initialize threads=8
+      @threads = threads
+      paths = which('usearch')
+      if paths.empty?
+        raise "usearch not found in path. Please ensure usearch is installed and aliased as 'usearch' in your path."
+      end
+      @cmd = paths.first
+    end
+
+    def custom_output_fields
+      " -userfields query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits+tcov"
+    end
+
+    def ublast query, target, evalue="1e-5"
+      subcmd = " -ublast #{query}"
+      subcmd += " -db #{target}"
+      subcmd += " -evalue #{evalue}"
+      blast6outfile = "#{File.basename(query)}_#{File.basename(target)}.b6"
+      subcmd += " -userout #{blast6outfile}"
+      subcmd += self.custom_output_fields
+      subcmd += " -strand both"
+      subcmd += " -threads #{@threads}"
+      self.run subcmd
+      blast6outfile
+    end
+
+    def makeudb_ublast filepath, output
+      subcmd = " -makeudb_ublast #{filepath}"
+      subcmd += " -output #{output}"
+      self.run subcmd
+    end
+
+    def findorfs filepath, output
+      subcmd = " -findorfs #{filepath}"
+      subcmd += " -output #{output}"
+      subcmd += " -xlat"
+      subcmd += " -orfstyle 7"
+      self.run subcmd
+    end
+
+    def run subcmd
+      subcmd += " -quiet"
+      `#{@cmd}#{subcmd}`
+    end
+
+  end # Usearch
+
+end # Transrate

data/lib/transrate/version.rb

@@ -0,0 +1,12 @@
+# encoding: utf-8
+
+module Transrate
+  module VERSION
+    MAJOR = 0
+    MINOR = 0
+    PATCH = 1
+    BUILD = nil
+
+    STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
+  end
+end # Transrate

data/transrate.gemspec

@@ -0,0 +1,28 @@
+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require File.expand_path('../lib/transrate/version', __FILE__)
+
+Gem::Specification.new do |gem|
+  gem.name          = 'transrate'
+  gem.authors       = [ "Richard Smith" ]
+  gem.email         = "rds45@cam.ac.uk"
+  gem.homepage      = 'https://github.com/blahah/assemblotron'
+  gem.summary       = %q{ quality assessment of de-novo transcriptome assemblies }
+  gem.description   = %q{ a library and command-line tool for quality assessment of de-novo transcriptome assemblies }
+  gem.version       = Transrate::VERSION::STRING.dup
+
+  gem.files = `git ls-files`.split("\n")
+  gem.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  gem.require_paths = %w[ lib ]
+
+  gem.add_dependency 'rake', '~> 10.1.0'
+  gem.add_dependency 'trollop', '~> 2.0'
+  gem.add_dependency 'which'
+  gem.add_dependency 'bio'
+  gem.add_dependency 'bettersam', '~> 0.0.1.alpha'
+
+  gem.add_development_dependency 'turn'
+  gem.add_development_dependency 'simplecov'
+  gem.add_development_dependency 'shoulda-context'
+  gem.add_development_dependency 'coveralls', '~> 0.6.7'
+end

metadata

@@ -0,0 +1,206 @@
+--- !ruby/object:Gem::Specification
+name: transrate
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Richard Smith
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-09-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: which
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bettersam
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.0.1.alpha
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.0.1.alpha
+- !ruby/object:Gem::Dependency
+  name: turn
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: shoulda-context
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.6.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.6.7
+description: ! ' a library and command-line tool for quality assessment of de-novo
+  transcriptome assemblies '
+email: rds45@cam.ac.uk
+executables:
+- transrate
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.md
+- bin/transrate
+- lib/transrate.rb
+- lib/transrate/assembly.rb
+- lib/transrate/bowtie2.rb
+- lib/transrate/comparative_metrics.rb
+- lib/transrate/rb_hit.rb
+- lib/transrate/read_metrics.rb
+- lib/transrate/reciprocal_annotation.rb
+- lib/transrate/usearch.rb
+- lib/transrate/version.rb
+- transrate.gemspec
+homepage: https://github.com/blahah/assemblotron
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: quality assessment of de-novo transcriptome assemblies
+test_files: []