transrate 1.0.0.alpha.5 → 1.0.0.alpha.8.bowtie

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3fc633cd9166010a55ea892edc4737c2f3221ccf
-  data.tar.gz: 2e9729a73f4128503d992b39c9711e15c89bae7b
+  metadata.gz: 0f6903da751cadec5102d2fa7e9c2381a9c39a25
+  data.tar.gz: bf9b30c2e334ae98ad6d959b085d521d43e5daf4
 SHA512:
-  metadata.gz: ef6f9cc4be67ec2b5d09fc9ab7487e3b21b0409e0af63752f33cf977e1d3f50f1644622af76cfba54d6b28c63b36a3607842d38ce0fdec51ff6c4d67063b571f
-  data.tar.gz: d4cc715ba05d3a332882a492fd99ea4ad79f48198dce550b7c1cefed3025663ff88ed7257554e9f4897fbb20f23c337135d72e6a8f3ac142182162875ff6dafa
+  metadata.gz: 97cdf2d6c922b1c0a901a1aa8f6e85013a8ec0c9cff54795b8bba3fa903efa7ef2ae4673c8e71e8ee292326eaadbf3ee617094c978a4fd39c836f6d8fb0d0672
+  data.tar.gz: 08ae932477980abe97b2b7fe874a14bd170688b1f8f60472971f21cc2ae0c7bb742d9a5c89ee923ccf5c476c4e59c5863a02a2e1994b4deb74e13e228e792136

data/bin/transrate

@@ -1,4 +1,5 @@
 #!/usr/bin/env ruby
+PROFILE = false
 
 require 'trollop'
 require 'transrate'
@@ -57,10 +58,9 @@ opts = Trollop::options do
   opt :outfile, "prefix filename to use for CSV output",
       :default => 'transrate'
   opt :loglevel, "the amount of information to print. " +
-                 "one of [error, info, warn, debug]",
+                 "one of [error, warn, info, debug]",
       :default => 'info'
   opt :install_deps, "install any missing dependencies"
-  opt :profile, "debug option: profile the code as it runs"
 end
 gem_dir = Gem.loaded_specs['transrate'].full_gem_path
 gem_deps = File.join(gem_dir, 'deps', 'deps.yaml')
@@ -111,7 +111,7 @@ if opts.left and opts.right
   end
 end
 
-if opts.profile
+if PROFILE
   logger.info "Starting profiler"
   RubyProf.start
 end
@@ -176,7 +176,7 @@ opts.assembly.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(1)} seconds"
 
   read_results = {}
 
@@ -269,7 +269,7 @@ CSV.open(outfile, 'wb') do |file|
   end
 end
 
-if opts.profile
+if PROFILE
   logger.info "Writing profiling results to transrate_profile.txt"
   result = RubyProf.stop
   printer = RubyProf::FlatPrinter.new(result)

data/deps/deps.yaml

@@ -25,16 +25,24 @@ blastplus:
     64bit:
       macosx: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-universal-macosx.tar.gz
       linux: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gz
-snap:
+bowtie2:
   binaries:
-    - snap
+    - bowtie2
+    - bowtie2-align-l
+    - bowtie2-align-s
+    - bowtie2-build
+    - bowtie2-build-l
+    - bowtie2-build-s
+    - bowtie2-inspect
+    - bowtie2-inspect-l
+    - bowtie2-inspect-s
   version:
-    number: '1.0beta.13'
-    command: 'snap'
+    number: '2.2.3'
+    command: 'bowtie2 --version'
   url:
     64bit:
-      linux: https://github.com/HibberdLab/snap/raw/master/bin/linux/snap.tar.gz
-      macosx: https://github.com/HibberdLab/snap/raw/osx_1.0beta.13/bin/macosx/snap.tar.gz
+      linux: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip
+      macosx: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-macos-x86_64.zip
 samtools:
   binaries:
     - samtools
@@ -50,7 +58,7 @@ bam-read:
   binaries:
    - bam-read
   version:
-    number: '0.3.2'
+    number: '0.3.4'
     command: 'bam-read'
   url:
     64bit:
@@ -61,7 +69,7 @@ bam-split:
   binaries:
    - bam-split
   version:
-    number: '0.1'
+    number: '0.2'
     command: 'bam-split'
   url:
     64bit:

data/lib/transrate/bowtie.rb

@@ -0,0 +1,103 @@
+module Transrate
+
+  class Bowtie2Error < StandardError
+  end
+
+  class Bowtie2
+
+    attr_reader :index_name, :sam, :read_count
+
+    def initialize
+      @bowtie2 = get_bin_path("bowtie2")
+      @bowtie2_build = get_bin_path("bowtie2-build")
+
+      @index_built = false
+      @index_name = ""
+    end
+
+    def get_bin_path bin
+      which_bin = Cmd.new("which #{bin}")
+      which_bin.run
+      if !which_bin.status.success?
+        raise IOError.new("ReadMetrics: could not find #{bin} in path")
+      end
+      which_bin.stdout.split("\n").first
+    end
+
+    def map_reads(file, left, right,
+                  insertsize: 200, insertsd: 50, threads: 8)
+      raise Bowtie2Error.new("Index not built") if !@index_built
+      lbase = File.basename(left.split(",").first)
+      rbase = File.basename(right.split(",").first)
+      index = File.basename(@index_name)
+      @sam = File.expand_path("#{lbase}.#{rbase}.#{index}.sam")
+      realistic_dist = insertsize + (5 * insertsd)
+      unless File.exists? @sam
+        # construct bowtie command
+        bowtiecmd = "#{@bowtie2} --very-sensitive"
+        bowtiecmd << " -x #{@index_name}"
+        bowtiecmd << " -a"
+        bowtiecmd << " -p #{threads} -X #{realistic_dist}"
+        bowtiecmd << " --no-unal"
+        bowtiecmd << " --seed 1337"
+        bowtiecmd << " --rdg 6,5"
+        bowtiecmd << " --rfg 6,5"
+        bowtiecmd << " --score-min L,-.6,-.4"
+        bowtiecmd << " -1 #{left}"
+        # paired end?
+        bowtiecmd << " -2 #{right}" if right
+        bowtiecmd << " -S #{@sam}"
+        # run bowtie
+        runner = Cmd.new bowtiecmd
+        runner.run
+        # parse bowtie output
+        if runner.stderr=~/([0-9]+)\ reads\;\ of\ these\:/
+          @read_count = $1.to_i
+          # save read_count to file
+          File.open("#{@sam}-read_count.txt", "wb") do |out|
+            out.write("#{@read_count}\n")
+          end
+        end
+        if !runner.status.success?
+          raise Bowtie2Error.new("Bowtie2 failed\n#{runner.stderr}")
+        end
+      else
+        @read_count = 0
+        if File.exist?("#{@sam}-read_count.txt")
+          @read_count = File.open("#{@sam}-read_count.txt").readlines.join.to_i
+        else
+          left.split(",").each do |l|
+            cmd = "wc -l #{l}"
+            count = Cmd.new(cmd)
+            count.run
+            if count.status.success?
+              @read_count += count.stdout.strip.split(/\s+/).first.to_i/4
+              File.open("#{@sam}-read_count.txt", "wb") do |out|
+                out.write("#{@read_count}\n")
+              end
+            else
+              logger.warn "couldn't get number of reads from #{l}"
+            end
+          end
+        end
+      end
+      @sam
+    end
+
+    def build_index file
+      @index_name = File.basename(file).split(".")[0..-2].join(".")
+      unless File.exists?(@index_name + '.1.bt2')
+        cmd = "#{@bowtie2_build} --quiet --offrate 1 #{file} #{@index_name}"
+        runner = Cmd.new cmd
+        runner.run
+        if !runner.status.success?
+          msg = "Failed to build Bowtie2 index\n#{runner.stderr}"
+          raise Bowtie2Error.new(msg)
+        end
+      end
+      @index_built = true
+    end
+
+  end # Bowtie2
+
+end # Transrate

data/lib/transrate/contig.rb

@@ -12,8 +12,7 @@ module Transrate
     # read-based metrics
     attr_accessor :eff_length, :eff_count, :tpm
     attr_accessor :coverage, :uncovered_bases, :p_uncovered_bases
-    attr_accessor :p_seq_true, :p_unique
-    attr_accessor :low_uniqueness_bases, :in_bridges
+    attr_accessor :p_seq_true, :p_unique, :in_bridges
     attr_accessor :p_good, :p_not_segmented
     # reference-based metrics
     attr_accessor :has_crb, :reference_coverage
@@ -30,7 +29,6 @@ module Transrate
       @in_bridges = 0
       @p_good = 0
       @p_seq_true = 0
-      @low_uniqueness_bases = 0
       @uncovered_bases = length
       @p_uncovered_bases = 1
       @p_unique = 0
@@ -227,10 +225,6 @@ module Transrate
       @p_uncovered_bases = n / length.to_f
     end
 
-    def p_unique_bases
-      (length - low_uniqueness_bases) / length.to_f
-    end
-
     # Contig score (product of all score components)
     def score
       return @score if @score != -1
@@ -238,8 +232,7 @@ module Transrate
         [p_bases_covered, 0.01].max.to_f * # proportion of bases covered
         [p_not_segmented, 0.01].max.to_f * # prob contig has 0 changepoints
         [p_good, 0.01].max.to_f * # proportion of reads that mapped good
-        [p_seq_true, 0.01].max.to_f * # scaled 1 - mean per-base edit distance
-        [p_unique, 0.01].max.to_f # prop mapQ >= 5
+        [p_seq_true, 0.01].max.to_f
       @score = [prod, 0.01].max
     end
   end

data/lib/transrate/express.rb

@@ -32,9 +32,7 @@ module Transrate
         runner = Cmd.new build_command(assembly, bamfile)
         runner.run
         unless runner.status.success?
-          raise ExpressError.new("Express failed\n" +
-                                 runner.stderr + "\n" +
-                                 runner.stdout)
+          abort "express failed on the bam file\n#{runner.stderr}"
         end
         File.rename(ex_output, fin_output)
       end
@@ -80,6 +78,20 @@ module Transrate
       expression
     end
 
+    # def fix_problem_snap_output bam
+    #   # express failed, probably because of temporary snap error
+    #   # convert bam to sam
+    #   sam = "#{File.expand_path(File.basename(bam, File.extname(bam)))}.sam"
+    #   Samtools.run "view -h #{bam} > #{sam}"
+    #   # run sam fixer on sam
+    #   checker = SamChecker.new
+    #   fixed_sam = "#{File.expand_path(File.basename(sam, File.extname(sam)))}.fixed.sam"
+    #   checker.fix_sam(sam, fixed_sam)
+    #   # convert sam to bam
+    #   Samtools.run "view -bS #{fixed_sam} > #{bam}"
+    #   bam
+    # end
+
   end # Express
 
  end # Transrate

data/lib/transrate/read_metrics.rb

@@ -11,7 +11,7 @@ module Transrate
 
     def initialize assembly
       @assembly = assembly
-      @mapper = Snap.new
+      @mapper = Bowtie2.new
       self.initial_values
 
       load_executables
@@ -47,29 +47,24 @@ module Transrate
       @read_length = get_read_length(left, right)
 
       # map reads
-      @mapper.build_index(@assembly.file, threads)
-      bamfile = @mapper.map_reads(@assembly.file, left, right,
+      @mapper.build_index(@assembly.file)
+      samfile = @mapper.map_reads(@assembly.file, left, right,
                                   insertsize: insertsize,
                                   insertsd: insertsd,
                                   threads: threads)
       @fragments = @mapper.read_count
+      bamfile = Samtools.sam_to_bam(samfile)
+      File.delete samfile
 
       # classify bam file into valid and invalid alignments
       sorted_bam = "#{File.basename(bamfile, '.bam')}.merged.sorted.bam"
-      readsorted_bam = "#{File.basename(bamfile, '.bam')}.valid.sorted.bam"
       merged_bam = "#{File.basename(bamfile, '.bam')}.merged.bam"
-      unless File.exist? sorted_bam
-        unless File.exist? readsorted_bam
-          valid_bam, invalid_bam = split_bam bamfile
-          readsorted_bam = Samtools.readsort_bam valid_bam
-          File.delete valid_bam
-        end
-      end
+      valid_bam, invalid_bam = split_bam bamfile
+      readsorted_bam = Samtools.readsort_bam valid_bam
 
       # pass valid alignments to eXpress for assignment
       # always have to run the eXpress command to load the results
       assigned_bam = assign_and_quantify readsorted_bam
-      File.delete readsorted_bam if File.exist? readsorted_bam
 
       # merge the assigned alignments back with the invalid ones
       unless File.exist? sorted_bam
@@ -142,12 +137,12 @@ module Transrate
         splitter = Cmd.new cmd
         splitter.run
         if !splitter.status.success?
-          logger.warn "Couldn't split bam file: #{bamfile}" +
+          raise StandardError.new "Couldn't split bam file: #{bamfile}" +
                       "\n#{splitter.stdout}\n#{splitter.stderr}"
         end
       end
       if !File.exist? valid
-        logger.warn "Splitting failed to create valid bam: #{valid}"
+        raise StandardError.new "Splitting failed to create valid bam: #{valid}"
       end
       [valid, invalid]
     end
@@ -162,7 +157,11 @@ module Transrate
     def analyse_expression express_output
       express_output.each_pair do |name, expr|
         contig = @assembly[name]
-        coverage = expr[:eff_count] * @read_length / expr[:eff_len]
+        if expr[:eff_len]==0
+          coverage = 0
+        else
+          coverage = expr[:eff_count] * @read_length / expr[:eff_len]
+        end
         @contigs_uncovered += 1 if coverage < 1
         @contigs_lowcovered += 1 if coverage < 10
         contig.coverage = coverage.round(2)
@@ -177,7 +176,7 @@ module Transrate
         csv_output = "#{File.basename(@assembly.file)}_bam_info.csv"
         csv_output = File.expand_path(csv_output)
 
-        analyse_bam bamfile, csv_output
+        analyse_bam(bamfile, csv_output)
         # open output csv file
         @potential_bridges = 0
 
@@ -188,7 +187,7 @@ module Transrate
         end
         @bad = @fragments_mapped - @good
       else
-        logger.warn "couldn't find bamfile: #{bamfile}"
+        raise "couldn't find bamfile: #{bamfile}"
       end
       @assembly.assembly.each_pair do |name, contig|
         @contigs_good += 1 if contig.score >= 0.5
@@ -217,7 +216,9 @@ module Transrate
         reader = Cmd.new cmd
         reader.run
         if !reader.status.success?
-          logger.warn "couldn't get information from bam file: #{bamfile}"
+          msg = "Couldn't get information from bam file: #{bamfile}\n"
+          msg << "#{reader.stdout}\n#{reader.stderr}"
+          raise msg
         end
       end
     end

data/lib/transrate/sam_checker.rb

@@ -0,0 +1,99 @@
+module Transrate
+
+  class SamChecker
+
+    def initialize
+      @contigs = {}
+      @reference = ""
+      @count = 0
+      @percent = 0
+      @first = true
+    end
+
+    def check sam
+      cols = sam.split("\t")
+
+      reference = cols[2]
+      length = @contigs[reference]
+
+      seq_length = cols[9].length
+      position = cols[3].to_i
+      cigar = cols[5]
+      # this generates a list of pairs in the form [ ["10", "M"], ["1", "D"] ]
+      list = cigar.split(/[MDIS]/).zip(cigar.scan(/[MDIS]/))
+      list.each_with_index do |a, i|
+        c=a[0].to_i
+        t=a[1]
+        if t=="M" or t=="D"
+          position += c
+        elsif i==0 and t=="S"
+          position += c
+        end
+      end
+      if position > length + 1
+        # `diff` is how much the cigar makes the read overlap the end
+        diff = position - (length + 1)
+        if list[-1][1] == "S" # the last item in the cigar is "S"
+          # increase the number in the last item in the cigar
+          list[-1][0] = (list[-1][0].to_i + diff).to_s
+          if list[-2][0].to_i > diff
+            # decrease the penultimate item in the cigar
+            list[-2][0] = (list[-2][0].to_i - diff).to_s
+          elsif list[-2][0].to_i == diff
+            # just delete the penultimate item if
+            list.delete_at(-2) # delete_at changes `list`
+          else
+            # this didn't happen in the rice/oases sam file, but it might
+          end
+        elsif list[-1][1] == "M"
+          if list[-1][0].to_i > diff
+            # decrease the number of the last item in the cigar
+            list[-1][0] = (list[-1][0].to_i - diff).to_s
+            # add a new soft mask item to the end of the cigar
+            list << [diff.to_s, "S"]
+          elsif list[-1][0].to_i == diff
+            # just change the last item to soft mask if it's the same length
+            # as the difference
+            list[-1][1] = "S"
+          end
+        end
+        cols[5] = list.join("")
+        return cols.join("\t")
+      else
+        return sam
+      end
+    end
+
+    def fix_sam input, output
+      sam1 = ""
+      File.open("#{output}", "wb") do |out|
+        File.open("#{input}").each_line do |sam|
+          if sam =~ /^@/
+            # header
+            # @SQ SN:Locus_1_Transcript_13/342_Confidence_1.000_Length_1605 LN:1605
+            if sam[0..2]=="@SQ"
+              cols = sam.split("\t")
+              name = cols[1][3..-1]
+              length = cols[2][3..-1].to_i
+              @contigs[name] = length
+            end
+            out.write sam
+          else
+            # alignment
+            if @first
+              sam1 = sam.dup
+              @first = false
+            else
+              out.write(check(sam1))
+              out.write(check(sam))
+              @first = true
+            end
+            @count+=1
+          end
+        end
+      end
+    end
+
+  end
+
+end

data/lib/transrate/snap.rb

@@ -5,6 +5,8 @@ module Transrate
 
   class Snap
 
+    require 'fix-trinity-output'
+
     attr_reader :index_name, :sam, :read_count
 
     def initialize
@@ -32,13 +34,14 @@ module Transrate
       cmd << " -s 0 1000" # min and max distance between paired-read starts
       cmd << " -H 300000" # max seed hits to consider in paired mode
       cmd << " -h 2000" # max seed hits to consider when reverting to single
-      cmd << " -I"   # ignore read IDs
       cmd << " -d 30" # max edit distance (function of read length?)
       cmd << " -t #{threads}"
       cmd << " -b" # bind threads to cores
       cmd << " -M"  # format cigar string
       cmd << " -sa" # keep all alignments, don't discard 0x100
-      # cmd << " -C++" # trim low-quality bases from front and back of reads
+      cmd << " -D 5" # edit distance to search for mapq calculation
+      cmd << " -om 5" # Output multiple alignments. extra edit distance
+      cmd << " -omax 10" # max alignments per pair/read
       cmd
     end
 
@@ -52,13 +55,19 @@ module Transrate
       @bam = File.expand_path("#{lbase}.#{rbase}.#{index}.bam")
       @read_count_file = "#{lbase}-#{rbase}-read_count.txt"
 
+      @fixer = Fixer.new # from the fix-trinity-output gem
       unless File.exists? @bam
         snapcmd = build_paired_cmd(left, right, threads)
         runner = Cmd.new snapcmd
         runner.run
         save_readcount runner.stdout
         unless runner.status.success?
-          raise SnapError.new("Snap failed\n#{runner.stderr}\n#{runner.stdout}")
+          if runner.stderr=~/Unmatched\sread\sIDs/
+            logger.warn "Unmatched read IDs. Fixing input files..."
+            remap_reads(left, right, threads)
+          else
+            raise SnapError.new("Snap failed\n#{runner.stderr}")
+          end
         end
       else
         load_readcount left
@@ -66,6 +75,30 @@ module Transrate
       @bam
     end
 
+    def remap_reads(left, right, threads)
+      fixedleft = []
+      fixedright = []
+      i = 0
+      left.split(",").zip(right.split(",")).each do |l, r|
+        prefix = "reads-#{i}"
+        @fixer.run(l, r, "#{prefix}")
+        fixedleft << "#{prefix}-fixed.1.fastq"
+        fixedright << "#{prefix}-fixed.2.fastq"
+        i+=1
+      end
+      left = fixedleft.join(",")
+      right = fixedright.join(",")
+      File.delete(@bam)
+      logger.info "Fixed input files"
+      snapcmd = build_paired_cmd(left, right, threads)
+      runner = Cmd.new snapcmd
+      runner.run
+      save_readcount runner.stdout
+      unless runner.status.success?
+        raise SnapError.new("Snap failed\n#{runner.stderr}")
+      end
+    end
+
     def save_readcount stdout
       stdout.split("\n").each do |line|
         cols = line.split(/\s+/)

data/lib/transrate/version.rb

@@ -11,7 +11,7 @@ module Transrate
     MAJOR = 1
     MINOR = 0
     PATCH = 0
-    BUILD = 'alpha.5'
+    BUILD = 'alpha.8.bowtie'
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
   end

data/lib/transrate.rb

@@ -8,12 +8,14 @@ require 'transrate/version'
 require 'transrate/contig'
 require 'transrate/assembly'
 require 'transrate/snap'
+require 'transrate/bowtie'
 require 'transrate/express'
 require 'transrate/read_metrics'
 require 'transrate/comparative_metrics'
 require 'transrate/contig_metrics'
 require 'transrate/samtools'
 require 'transrate/cmd'
+require 'transrate/sam_checker'
 require 'transrate/transrate.so'
 
 # Transrate is a comprehensive transcriptome assembly

data/test/data/bridging_reads.l.fastq

@@ -1,20 +1,20 @@
-@read1:1
+@read1/1
 AAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGGGG
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read2:1
+@read2/1
 CACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCA
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read3:1
+@read3/1
 CACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCA
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read4:1
+@read4/1
 CTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGG
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read5:1
+@read5/1
 ACGACGCGCACCACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGC
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg

data/test/data/bridging_reads.r.fastq

@@ -1,20 +1,20 @@
-@read1:2
+@read1/2
 AGGCCGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGC
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read2:2
+@read2/2
 GGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGT
 +
 ggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read3:2
+@read3/2
 CGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTAT
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read4:2
+@read4/2
 ACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGCTAAG
 +
 ggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
-@read5:2
+@read5/2
 GGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGC
 +
 gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg

data/test/test_bin.rb

@@ -24,7 +24,11 @@ class TestTransrateBin < Test::Unit::TestCase
       "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"]
+      "150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.merged.sorted.bam",
+      "150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.merged.valid.bam",
+      "150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.valid.bam",
+      "150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.valid.sorted.bam",
+      "150uncovered.l.fq.150uncovered.r.fq.sorghum_transcript.sam-read_count.txt"]
       files.each do |file|
         File.delete(file) if File.exist?(file)
       end
@@ -66,6 +70,10 @@ class TestTransrateBin < Test::Unit::TestCase
       assert File.exist?("transrate_sorghum_transcript.fa_contigs.csv"),
              "contig csv file doesn't exist"
       hash = {}
+      if !c.status.success?
+        puts c.stderr
+        puts c.stdout
+      end
       CSV.foreach("transrate_assemblies.csv", :headers => true,
                                    :header_converters => :symbol,
                                    :converters => :all) do |row|

data/test/test_read_metrics.rb

@@ -27,23 +27,36 @@ class TestReadMetrics < Test::Unit::TestCase
       left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
       right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
       Dir.mktmpdir do |tmpdir|
+      # tmpdir = Dir.mktmpdir
+      # puts 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 217,     stats[:fragments_mapped], 'number mapping'
-          assert_equal 0.9731,   stats[:p_fragments_mapped].round(4),
+          assert_equal 219,     stats[:fragments_mapped], 'number mapping'
+          assert_equal 0.9821,   stats[:p_fragments_mapped].round(4),
                        'proportion mapping'
-          assert_equal 129,     stats[:good_mappings], 'good mapping'
-          assert_equal 0.5785,   stats[:p_good_mapping].round(4),
+          assert_equal 184,     stats[:good_mappings], 'good mapping'
+          assert_equal 0.8251,   stats[:p_good_mapping].round(4),
                        'percent good mapping'
-          assert_equal 88,      stats[:bad_mappings], 'bad mapping'
-          assert_equal 2, stats[:potential_bridges], 'bridges'
+          assert_equal 35,      stats[:bad_mappings], 'bad mapping'
+        end
+      end
+    end
+
+    should "calculate more read mapping statistics" do
+      left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
+      right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          @read_metrics.run(left, right)
+          stats = @read_metrics.read_stats
+          assert_equal 0, 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 0, stats[:contigs_good], 'good contigs'
+          assert_equal 1, stats[:contigs_good], 'good contigs'
         end
       end
     end
@@ -63,22 +76,22 @@ class TestReadMetrics < Test::Unit::TestCase
 
           edit_a = a[:p_seq_true].round(5)
           edit_b = b[:p_seq_true].round(5)
-          assert_equal 0.98342, edit_a, "edit distance 1"
-          assert_equal 0.96645, edit_b, "edit distance 2"
+          assert_equal 0.98618, edit_a, "edit distance 1"
+          assert_equal 0.9749, edit_b, "edit distance 2"
 
-          assert_equal 0.59524, a[:p_good].round(5), "proportion of good mappings"
-          assert_equal 0.59398, b[:p_good].round(5), "proportion of good mappings"
+          assert_equal 0.83146, a[:p_good].round(5), "proportion of good mappings"
+          assert_equal 0.84615, b[:p_good].round(5), "proportion 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 2, unc_b, "uncovered bases"
+          assert_equal 12, unc_a, "uncovered bases"
+          assert_equal 4, unc_b, "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 0.99757, prop_unc_b.round(5), "proportion covered bases"
+          assert_equal 0.98361, prop_unc_a.round(5), "proportion covered bases"
+          assert_equal 0.99514, prop_unc_b.round(5), "proportion covered bases"
 
         end
       end
@@ -99,8 +112,8 @@ class TestReadMetrics < Test::Unit::TestCase
 
           edit_a = a[:p_not_segmented].round(5)
           edit_b = b[:p_not_segmented].round(5)
-          assert_equal 0.11444, edit_a, "probability not segmented 1"
-          assert_equal 0.82779, edit_b, "probability not segmented 2"
+          assert_equal 0.47635, edit_a, "probability not segmented 1"
+          assert_equal 0.77451, edit_b, "probability not segmented 2"
 
         end
       end

data/test/test_transrater.rb

@@ -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 0.10231, score.round(5) # regression test
+          assert_equal 0.4078, score.round(5) # regression test
         end
       end
     end

data/transrate.gemspec

@@ -23,6 +23,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
   gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.2'
   gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'
+  gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
 
   gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
   gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.5
+  version: 1.0.0.alpha.8.bowtie
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,258 +9,278 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-22 00:00:00.000000000 Z
+date: 2014-11-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '2.0'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 2.0.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '2.0'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 2.0.4
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '2.0'
 - !ruby/object:Gem::Dependency
   name: bindeps
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.1'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.1.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.1'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.1.3
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
 - !ruby/object:Gem::Dependency
   name: crb-blast
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.4.2
 - !ruby/object:Gem::Dependency
   name: ruby-prof
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.15'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.15.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.15'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.15.1
+- !ruby/object:Gem::Dependency
+  name: fix-trinity-output
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '10.3'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 10.3.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '10.3'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 10.3.2
 - !ruby/object:Gem::Dependency
   name: rake-compiler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.9.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.9.2
 - !ruby/object:Gem::Dependency
   name: turn
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.9.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.9.7
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 4.7.5
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 4.7.5
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.8'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.8.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.8'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.8.2
 - !ruby/object:Gem::Dependency
   name: shoulda-context
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.2.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.2.1
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '0.7'
-description: " a library and command-line tool for quality assessment of de-novo transcriptome
-  assemblies "
+description: ' a library and command-line tool for quality assessment of de-novo transcriptome
+  assemblies '
 email: rds45@cam.ac.uk
 executables:
 - transrate
@@ -268,8 +288,8 @@ extensions:
 - ext/transrate/extconf.rb
 extra_rdoc_files: []
 files:
-- ".gitignore"
-- ".travis.yml"
+- .gitignore
+- .travis.yml
 - Gemfile
 - LICENSE
 - README.md
@@ -281,12 +301,14 @@ files:
 - ext/transrate/transrate.c
 - lib/transrate.rb
 - lib/transrate/assembly.rb
+- lib/transrate/bowtie.rb
 - lib/transrate/cmd.rb
 - 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/snap.rb
 - lib/transrate/transrater.rb
@@ -325,18 +347,19 @@ require_paths:
 - ext
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - '>'
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.1.4
 signing_key: 
 specification_version: 4
 summary: quality assessment of de-novo transcriptome assemblies
 test_files: []
+has_rdoc: