lederhosen 1.4.0 → 1.6.0

data/Gemfile

@@ -1,6 +1,6 @@
 source :rubygems
 
-gem 'dna', '0.0.12'
+gem 'dna', '0.1.2'
 gem 'progressbar'
 gem 'thor'
 

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.4.0"
+  s.version = "1.6.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
@@ -36,6 +36,7 @@ Gem::Specification.new do |s|
     "lib/lederhosen/tasks/split_fasta.rb",
     "lib/lederhosen/tasks/trim.rb",
     "lib/lederhosen/tasks/version.rb",
+    "lib/lederhosen/trimmer.rb",
     "lib/lederhosen/version.rb",
     "readme.md",
     "spec/cli_spec.rb",
@@ -43,10 +44,11 @@ Gem::Specification.new do |s|
     "spec/data/ILT_L_9_B_001_3.txt.gz",
     "spec/data/ILT_L_9_B_002_1.txt.gz",
     "spec/data/ILT_L_9_B_002_3.txt.gz",
+    "spec/data/example.fastq",
     "spec/data/test.uc",
-    "spec/misc_spec.rb",
     "spec/no_tasks_spec.rb",
-    "spec/spec_helper.rb"
+    "spec/spec_helper.rb",
+    "spec/trimmer_spec.rb"
   ]
   s.homepage = "http://audy.github.com/lederhosen"
   s.licenses = ["MIT"]
@@ -58,7 +60,7 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<dna>, ["= 0.0.12"])
+      s.add_runtime_dependency(%q<dna>, ["= 0.1.2"])
       s.add_runtime_dependency(%q<progressbar>, [">= 0"])
       s.add_runtime_dependency(%q<thor>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
@@ -66,7 +68,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<jeweler>, [">= 0"])
       s.add_development_dependency(%q<ruby-prof>, [">= 0"])
     else
-      s.add_dependency(%q<dna>, ["= 0.0.12"])
+      s.add_dependency(%q<dna>, ["= 0.1.2"])
       s.add_dependency(%q<progressbar>, [">= 0"])
       s.add_dependency(%q<thor>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
@@ -75,7 +77,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<ruby-prof>, [">= 0"])
     end
   else
-    s.add_dependency(%q<dna>, ["= 0.0.12"])
+    s.add_dependency(%q<dna>, ["= 0.1.2"])
     s.add_dependency(%q<progressbar>, [">= 0"])
     s.add_dependency(%q<thor>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])

data/lib/lederhosen/tasks/trim.rb

@@ -13,39 +13,59 @@ module Lederhosen
     method_option :reads_dir, :type => :string, :required => true
     method_option :out_dir,   :type => :string, :required => true
     method_option :pretrim,   :type => :numeric, :default => 11
+    method_option :read_type, :type => :string, :default => 'qseq'
+    method_option :min_length, :type => :numeric, :default => 75
 
     def trim
-      raw_reads = options[:reads_dir]
-      out_dir   = options[:out_dir]
-      pretrim   = options[:pretrim]
+      raw_reads  = options[:reads_dir]
+      out_dir    = options[:out_dir]
+      pretrim    = options[:pretrim]
+      read_type  = options[:read_type]
+      min_length = options[:min_length]
 
       ohai "trimming #{File.dirname(raw_reads)} and saving to #{out_dir}"
-
       run "mkdir -p #{out_dir}"
 
-      raw_reads = get_grouped_qseq_files raw_reads
+      raw_reads =
+        if read_type == 'qseq'
+          get_grouped_qseq_files(raw_reads)
+        elsif read_type == 'fastq'
+          r = Dir[raw_reads].map do |x|
+            [ File.basename(x, '.fastq'), x ]
+          end
+          Hash[r]
+        end
+
+      if raw_reads.size == 0
+        ohno 'glob matches no reads'
+      end
+
+      raw_reads.map do |prefix, files|
 
-      ohai "found #{raw_reads.length} pairs of reads"
+        # get an output handle
+        out = File.join(out_dir, "#{File.basename(prefix)}.fasta")
+
+        # create the trimmed sequence generator
+        trimmer =
+          if read_type == 'qseq'
+            Trimmer::QSEQTrimmer.new(*files)
+          elsif read_type == 'fastq'
+            Trimmer::InterleavedTrimmer.new(files)
+          end
+
+        # trim and write
+        File.open(out, 'w') do |o|
+          trimmer.each do |trimmed_record|
+            o.puts trimmed_record
+          end
+        end # File.open
 
-      pbar = ProgressBar.new "trimming", raw_reads.length
-      raw_reads.each do |a|
-        pbar.inc
-        out = File.join(out_dir, "#{File.basename(a[0])}.fasta")
-        # TODO get total and trimmed
-        total, trimmed = trim_pairs a[1][0], a[1][1], out, :min_length => 70
       end
-      pbar.finish
 
     end
 
     no_tasks do
 
-      # reverse complement a DNA sequence
-      # assumes only GATCN nucleotides
-      def reverse_complement(s)
-        s.reverse.tr('GATCNgatcn','CTAGNctagn')
-      end
-
       # Function for grouping qseq files produced by splitting illumina
       # reads by barcode
       #
@@ -55,81 +75,7 @@ module Lederhosen
         Dir.glob(glob).group_by { |x| File.basename(x).split('_')[0..4].join('_') }
       end
 
-      # Trim a pair of QSEQ files. Saves to a single,
-      # interleaved .fasta file
-      def trim_pairs(left, right, out, args={})
-        cutoff     = args[:cutoff]     || 20
-        min_length = args[:min_length] || 70
-
-        left_handle, right_handle =
-          begin
-            [ Zlib::GzipReader.open(left), Zlib::GzipReader.open(right)]
-          rescue Zlib::GzipFile::Error
-            [ File.open(left), File.open(right) ]
-          end
-
-        out_handle   = File.open out, 'w'
-
-        left_reads  = Dna.new left_handle
-        right_reads = Dna.new right_handle
-
-        i = 0
-        left_reads.zip(right_reads).each do |a, b|
-          i += 1
-          seqa = trim_seq a
-          seqb = trim_seq b
-          unless [seqa, seqb].include? nil
-            if seqb.length >= min_length && seqa.length >= min_length
-              seqb = reverse_complement(seqb)
-              out_handle.puts ">#{i}:0\n#{seqa}\n>#{i}:1\n#{seqb}"
-            end
-          end
-        end
-        left_handle.close
-        right_handle.close
-        out_handle.close
-      end
-
-      # Return longest subsequence with quality scores
-      # greater than min. (Illumina PHRED)
-      # Trim2 from Huang, et. al
-      # returns just the sequence
-      def trim_seq(dna, args={})
-
-
-        pretrim = args[:pretrim] || false
-        # trim primers off of sequence
-        # XXX this is experiment-specific and needs to be made
-        # into a parameter
-        if pretrim
-          dna.sequence = dna.sequence[pretrim..-1]
-          dna.quality  = dna.quality[pretrim..-1]
-        end
-
-        # throw away any read with an ambiguous primer
-        return nil if dna.sequence =~ /N/
-
-        min    = args[:min]    || 20 # what is this constant?
-        offset = args[:cutoff] || 64 # XXX depends on sequencing tech.
-
-        _sum, _max, first, last, start, _end = 0, 0, 0, 0, 0
-
-        dna.quality.each_byte.each_with_index do |b, a|
-          _sum += (b - offset - min)
-          if _sum > _max
-            _max = _sum
-            _end = a
-            start = first
-          elsif _sum < 0
-            _sum = 0
-            first = a
-          end
-        end
-
-        # XXX why is this rescue statement here?
-        dna.sequence[start + 11, _end - start].gsub('.', 'N') rescue nil
-      end
-    end
+    end # no_tasks
 
   end
 end

data/lib/lederhosen/trimmer.rb

@@ -0,0 +1,126 @@
+module Lederhosen
+module Trimmer
+
+# Base class for trimming paired-end reads
+class PairedTrimmer < Enumerator
+  def initialize(paired_iterator, args = {})
+    @paired_iterator = paired_iterator
+    @pretrim         = args[:pretrim]
+    @min_length      = args[:min_length] || 70
+  end
+
+  def each(&block)
+    @paired_iterator.each_with_index do |a, i|
+      seqa = trim_seq a[0], :pretrim => @pretrim
+      seqb = trim_seq a[1], :pretrim => @pretrim
+      unless [seqa, seqb].include? nil
+        if seqb.length >= @min_length && seqa.length >= @min_length
+          seqb = reverse_complement(seqb) # experiment-specific?
+          a = Fasta.new :name => "#{i}:0", :sequence => seqa
+          b = Fasta.new :name => "#{i}:1", :sequence => seqb
+          block.yield a
+          block.yield b
+        else # we just skip bad reads entirely
+          next
+        end
+      else
+        next
+      end
+    end
+  end
+
+  # reverse complement a DNA sequence
+  # assumes only GATCN nucleotides
+  def reverse_complement(s)
+    s.reverse.tr('GATCNgatcn','CTAGNctagn')
+  end
+
+  # this method does the actual trimming. It is a class method
+  # so you can use it if you don't want to initialize a PairedTrimmer
+  def trim_seq(dna, args={})
+    pretrim = args[:pretrim] || false
+
+    # trim primers off of sequence
+    # XXX this is experiment-specific and needs to be made
+    # into a parameter
+    if pretrim
+      dna.sequence = dna.sequence[pretrim..-1]
+      dna.quality  = dna.quality[pretrim..-1]
+    end
+
+    dna.sequence.gsub! '.', 'N'
+
+    min    = args[:min]    || 20 # what is this constant?
+    offset = args[:cutoff] || 64 # XXX depends on sequencing tech.
+
+    _sum, _max, first, last, start, _end = 0, 0, 0, 0, 0
+
+    dna.quality.each_byte.each_with_index do |b, a|
+      _sum += (b - offset - min)
+      if _sum > _max
+        _max = _sum
+        _end = a
+        start = first
+      elsif _sum < 0
+        _sum = 0
+        first = a
+      end
+    end
+
+    dna.sequence[start, _end - start] rescue nil
+  end
+
+end
+
+#
+# Yields trimmed fasta records given an input
+# interleaved, paired-end fastq file
+class InterleavedTrimmer < PairedTrimmer
+
+  def initialize(interleaved_file, args = {})
+    # create an iterator that yields paired records
+    # as an array
+
+    handle =
+      begin
+        Zlib::GzipReader.open(interleaved_file)
+      rescue Zlib::GzipFile::Error
+        File.open(interleaved_file)
+      end
+
+    reads = Dna.new handle
+    iterator = reads.each_slice(2)
+
+    super(iterator, args)
+
+  end
+end
+
+# Yield trimmed fasta records given an two separate
+# paired QSEQ files
+class QSEQTrimmer < PairedTrimmer
+  def initialize(left_file, right_file, args = {})
+    # create an iterator that yields paired records
+    # as an array
+
+    left_handle, right_handle =
+      begin
+        [ Zlib::GzipReader.open(left_file), Zlib::GzipReader.open(right_file)]
+      rescue Zlib::GzipFile::Error
+        [ File.open(left_file), File.open(right_file) ]
+      end
+
+    left_file_reads  = Dna.new left_handle
+    right_reads = Dna.new right_handle
+
+    iterator = left_file_reads.zip(right_reads)
+
+    super(iterator, args)
+
+    left_handle.close
+    right_handle.close
+  end
+end
+
+end # module Trimmer
+end # module Lederhosen

data/lib/lederhosen/version.rb

@@ -1,8 +1,8 @@
 module Lederhosen
   module Version
     MAJOR = 1
-    MINOR = 4
-    CODENAME = 'Strickjacke' # changes for minor versions
+    MINOR = 6
+    CODENAME = 'Sauerkraut' # changes for minor versions
     PATCH = 0
 
     STRING = [MAJOR, MINOR, PATCH].join('.')

data/lib/lederhosen.rb

@@ -6,16 +6,3 @@ require 'progressbar'
 require 'thor'
 
 Dir.glob(File.join(File.dirname(__FILE__), 'lederhosen', '*.rb')).each { |f| require f }
-
-##
-# Here I extend the string class to add the to_kmers method
-#
-# Does it really need to be a method of String? Sure, why not?
-#
-class String
-  def to_kmers(k)
-    return [] if k == 0
-    k -= 1
-    (0..(self.length-k-1)).collect { |i| self[i..i+k] }
-  end
-end

data/readme.md

@@ -38,12 +38,16 @@ Lederhosen is invoked by typing `lederhosen [TASK]`
 
 ### Trim Reads
 
-Trim (Illumina) reads using quality scores. Output will be a directory of fasta files. Reads can optionally be gzipped.
+Trim (Illumina, QSEQ format) reads using quality scores. Output will be a directory of fasta files. Reads can optionally be gzipped.
 
     lederhosen trim --reads_dir=reads/*.txt --out_dir=trimmed/
 
 The trimming process will reverse complement the "right" pair so that both reads are in the forward orientation.
 
+You can also trim interleaved, paired-end FASTQ files:
+
+    lederhosen trim --reads_dir=reads/*.fastq --out_dir=trimmed/ read-type='fastq'
+
 ### Create Database
 
 Create UDB database required by usearch from TaxCollector
@@ -65,6 +69,7 @@ lederhosen cluster \
   --output=clusters_95.uc \
   --database=taxcollector.udb
 ```
+
 ### Generate OTU table(s)
 
 Create an OTU abundance table where rows are samples and columns are clusters. The entries are the number of reads for that cluster in a sample.

data/spec/cli_spec.rb

@@ -12,11 +12,16 @@ describe Lederhosen::CLI do
     $?.success?.should be_true
   end
 
-  it 'should trim reads' do
+  it 'should trim paired QSEQ reads' do
     `./bin/lederhosen trim --reads-dir=spec/data/IL*.txt.gz --out-dir=#{$test_dir}/trimmed`
     $?.success?.should be_true
   end
 
+  it 'should trim paired, interleaved FASTQ reads' do
+    `./bin/lederhosen trim --reads-dir=spec/data/example.fastq --out-dir=#{$test_dir}/trimmed --read-type fastq`
+    $?.success?.should be_true
+  end
+
   it 'can create a usearch udb using usearch' do
     `./bin/lederhosen make_udb --input #{$test_dir}/trimmed/ILT_L_9_B_001.fasta --output #{$test_dir}/test_db.udb`
     $?.success?.should be_true

data/spec/data/example.fastq

@@ -0,0 +1,400 @@
+@HWUSI-EAS163FR:13:1:13:8520:20401:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGGAGGAGCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:8520:20401:0:1:1
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+@HWUSI-EAS163FR:13:1:13:11817:20423:0:1:1
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++HWUSI-EAS163FR:13:1:13:11817:20423:0:1:1
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++HWUSI-EAS163FR:13:1:13:17330:20421:0:1:1
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+@HWUSI-EAS163FR:13:1:13:17330:20421:0:3:1
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++HWUSI-EAS163FR:13:1:13:17330:20421:0:3:1
+aBBB_aaaaa\BBBZ_`__\hehhghhhhfhhhhhghhhgggehghgahhghahheff]daaW]f]dffW]ccc]eeehchhfghfa^Lb^W]``
+@HWUSI-EAS163FR:13:1:13:17318:20444:0:1:1
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++HWUSI-EAS163FR:13:1:13:17318:20444:0:1:1
+ggggggggggfgggggggggggggeffff[`adadggggg_fcfffedfdgfgggf_affedfdfWfdfdcfWcfbRb_]bbb`beg_]ceebecdaeac]
+@HWUSI-EAS163FR:13:1:13:17318:20444:0:3:1
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++HWUSI-EAS163FR:13:1:13:17318:20444:0:3:1
+^BBBV_aa_UTBBBTZ_\_Yghhhcfffdffh_hhffddf_ffffadffeff_[edffdbcaaWc_W]b_Z`Z\`]``b`ehfefcW_W__a_aa
+@HWUSI-EAS163FR:13:1:13:7273:20455:0:1:1
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++HWUSI-EAS163FR:13:1:13:7273:20455:0:1:1
+hhhhhhhhhhhhhhhhhhghhhhghadffZaccc`hggfhfhffh_[^bLW\XX[a_cc_badccV^X_Y\`Y\^a\__^aaZWaaa\ebadac_ZZ`V_^
+@HWUSI-EAS163FR:13:1:13:7273:20455:0:3:1
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++HWUSI-EAS163FR:13:1:13:7273:20455:0:3:1
+^BBBWX^_ZWWBBBTW_W]XhhehhfhhhdehchhhhhhhhhhhhY`B``\^\\^hhhfgghgdfa]ddec[dfadedccfdfcbb]Lbb\^_^_
+@HWUSI-EAS163FR:13:1:13:10932:20593:0:1:1
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++HWUSI-EAS163FR:13:1:13:10932:20593:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhhehhdehhhdhghghfhghhhahhhchhhhhdhhdaaffe^b`b`^b^`bdadddddb_eabadbcece_][`_`\
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++HWUSI-EAS163FR:13:1:13:10932:20593:0:3:1
+aBBBX\a\\^\BBBZY_Z_Yeffffhhhhgchhhhhgfgghhhgh_`B`a``_`bfdhhfdegchfffegddffffffdfhdfabdcadd]cac`
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++HWUSI-EAS163FR:13:1:13:9788:20737:0:1:1
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+^BBBU]]_]][BBBZ^````ghhghhhhhhgghhhhgghhhhhhg_bBbbbb```bgggdSDFFPRHUPOcdadddcdeffddbaedbaaX_Oa_
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++HWUSI-EAS163FR:13:1:13:9788:20763:0:1:1
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++HWUSI-EAS163FR:13:1:13:9788:20763:0:3:1
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++HWUSI-EAS163FR:13:1:13:15892:20797:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhhghh[fcffdhhhhhfhghhfbfffdhhhhfddfdddhhf_fafa`b]`bcaca_ddbaedaaee_dada__aac_
+@HWUSI-EAS163FR:13:1:13:15892:20797:0:3:1
+GNNNACTACGGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:15892:20797:0:3:1
+aBBB[_a__\_BBBW\a^a\ghhhghhhhhghahhhhfchhhhhgbgfggghffhfgghfecdae[a_aa_dRbacdddedbfddd`\da[baab
+@HWUSI-EAS163FR:13:1:13:6920:20815:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATCATTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTCAAAAGTTC
++HWUSI-EAS163FR:13:1:13:6920:20815:0:1:1
+hhhhhhhhhhhhhhhhhhfhghhhheghhddfeddhgggghgfhhb^^bH^^^`^fdgdffdfcgaeccaaddacaaaa`a^a`d_^\`^\UQNX^\_^_]
+@HWUSI-EAS163FR:13:1:13:6920:20815:0:3:1
+GNNNACTACGCNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGNCTCAGCGTCAGTTTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:13:6920:20815:0:3:1
+aBBB[_aa_a]BBBXZ`]__hhghafhhdhfhhhhhhgfhhhhhhbdBdd`bdbeghhhgghgghffghhcadhadededhchafbabddHb_b^
+@HWUSI-EAS163FR:13:1:13:17972:20814:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGATCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:17972:20814:0:1:1
+hhhhhhhhhhhhhhhhhhghhhhhhhgahggghhghhhghhhghhgehhhfhhhhabdfdbdhgebedhcahadhdadccddcbddfdddfheeaaabbdd
+@HWUSI-EAS163FR:13:1:13:17972:20814:0:3:1
+GNNNACTACGCNNNTATCTAANCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:17972:20814:0:3:1
+aBBBYaaaa\_BBBYZ`__]dBeeeddeeeghghhfghhhhhhhhghhhhhhhfhfhhghfhhfhdggfdhgffhbdghdhfffeacddbcccdd
+@HWUSI-EAS163FR:13:1:13:7991:20840:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTGATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:7991:20840:0:1:1
+hhhhhhhhhhhhhhhhhhfhhhhhhhghhffhhhfgggfhfhghh`_`bH\_^^^cdhgfecgffagdgabd_bddadcadebcc`a]aaddadaa]a`aa
+@HWUSI-EAS163FR:13:1:13:7991:20840:0:3:1
+GNNNACTACGGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGNCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:7991:20840:0:3:1
+aBBB_aaaaa`BBB\\aaaahhhhhhhhhhgghhhhhhhhhhhhhbdBfdddbbdhghghhfafhhehehfbddghhgdhhdffgeedde[a_d_
+@HWUSI-EAS163FR:13:1:13:17959:20835:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGATCGTAGATGGATGTTTACGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:17959:20835:0:1:1
+cffffffffffafff]fWffcfQff`ZK`YcX^aWbbb`b[accf]W_ffOd]YJJZ^^Z_a_fYIYYZYP[G^^VURVZaWWG^QSGVS]b^BBBBBBBB
+@HWUSI-EAS163FR:13:1:13:17959:20835:0:3:1
+GNNNACTACGCNNNTATCTAANCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCCATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:17959:20835:0:3:1
+\BBBVaa^^aaBBB^Z`__]dBeeeceedeacfffSfdefhhhcggh_fgffef]affc]fafcf]ffaf[cfRa_c]c]cW_cJ^d^[W\YQ[]
+@HWUSI-EAS163FR:13:1:13:14495:20882:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:13:14495:20882:0:1:1
+hhhhhhhhhhhhhhhhhhghhhhhhhghhfhhgghhhgfhgghhhhchhhhhgegfghfhhfhhhgfgegbfgdgffbdddd[ffdddf_dfdfcdc`ade
+@HWUSI-EAS163FR:13:1:13:14495:20882:0:3:1
+GNNNACTACGCNNNTATCTAATCCTGTTTGCTCCCCACGCTTTCGCANCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:13:14495:20882:0:3:1
+aBBB_bbbbbbBBB]^aaaahhhhhhhhhhhhghhhchhhhhhhgbbBddbbbbdhchhhhghghdhgdhffchgeffgfbgdcgeddb[__b_b
+@HWUSI-EAS163FR:13:1:13:2382:20888:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATCGGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:13:2382:20888:0:1:1
+hhhhhhhhhhhhhhhghhhhhhhhhe_ffdffcc`hghghhggehh_bhhehgffhdfggacfdhdhgheahgbggffbhgda]dbbbbaa[d_[^Qb_`R
+@HWUSI-EAS163FR:13:1:13:2382:20888:0:3:1
+GNNNACTACGGNNNTATCTAATCCCGTNCGCTCCCCTGGCTTTCGCGNCTCAGCGTCAGTTTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:13:2382:20888:0:3:1
+aBBBXaa^aaaBBBX^aaaahhhhheeBbededeegggaafhhhgdfBbb`ad`adfaffgghc[cf_]fW[`d_ehWcadehhd_aPbbM`]a^
+@HWUSI-EAS163FR:13:1:13:4259:20898:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:4259:20898:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhfdffcffffchghghfhghhfaff_afccfhchhdcafcfafafaafaffeaeedeedaeaaaddeecdaa_dadb
+@HWUSI-EAS163FR:13:1:13:4259:20898:0:3:1
+GNNNACTACGGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGNCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:4259:20898:0:3:1
+aBBB]aaaa^`BBB\[a^a^hhhhhfcfffT[F[]SXXTVhhhhfbbBdddbbbbghhhfhhhahhhgfhdfbafdfffchd]_cadbac_a\a_
+@HWUSI-EAS163FR:13:1:13:3280:20911:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATCAGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:13:3280:20911:0:1:1
+hhhhhhhhhhhhhhhhhhghhhhhhdeffdhhhddhdhghhhgghhabhhcheehgfhdffdghhghcggbheahdaabddaa^edcdedcce__a\aaa_
+@HWUSI-EAS163FR:13:1:13:3280:20911:0:3:1
+GNNNACTACCGNNNTATCTAATCCCGTNCGCTCCCCTGGCTTTCGCGNCTCAGCGTCAGTTTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:13:3280:20911:0:3:1
+`BBB]]IZ]]aBBBW^aaaaghhhhedBeedeeeeh]hhhhhhhaddBeedbddfhhhhghhheheghgghdcfdhchghhghehceehh_hddd
+@HWUSI-EAS163FR:13:1:13:4054:20949:0:1:1
+TGTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTT
++HWUSI-EAS163FR:13:1:13:4054:20949:0:1:1
+ffcffdcddLZaaaac_ccadbdb]aaOaaW\[^aY`]a^fffccddXb]dOd__dd`dd``Wddd^d\dXH\GPaaW^^``d[^a\ZWd^^b]bWXW^Zd
+@HWUSI-EAS163FR:13:1:13:4054:20949:0:3:1
+GNNNACTACCGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGNCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:4054:20949:0:3:1
+^BBBW]_\[ZZBBBT\a^a\hhhhhe\eeeadaddfffffhhhhhbdB`bbbbbdgghhhfhhdhdggghfcegfhhfdcdchdgdedgd_daca
+@HWUSI-EAS163FR:13:1:13:4704:21006:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATGATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCC
++HWUSI-EAS163FR:13:1:13:4704:21006:0:1:1
+hhhhhhhhhhhhhhhhhhehfhhhheefffafcfffefdfhehhhb_`dH]aaa_gdhdcddgghdgdhcdhgdgbddcdccgad^aaac_d_a]_\_^\a
+@HWUSI-EAS163FR:13:1:13:4704:21006:0:3:1
+GNNNACTACAGNNNTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTNCTCAGCGTCAGTAACGGCCCAGAGACCTGCCTTCGCCATTGGTGTTC
++HWUSI-EAS163FR:13:1:13:4704:21006:0:3:1
+]BBBXY____`BBBY^a^aahehhhhhhhhghchhhhhhghhhffddBddd`dadehhhggggheghggfafdhdcddddhhhdgacWdbadadc
+@HWUSI-EAS163FR:13:1:13:15502:21011:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:13:15502:21011:0:1:1
+hhhhhhhhhhhhhhhhghfhhhghhfbffcZdbbbeddbehffhhhefhhfffhfffhfgfcgchfffffdfdcgfcdcc__T_ca\]a]`dac`a_^a_d
+@HWUSI-EAS163FR:13:1:13:15502:21011:0:3:1
+GNNNACTACGGNNNTATCTAANCCTGTTTGCTCCCCACGCTTTCGCANCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:13:15502:21011:0:3:1
+aBBB^aa_^a_BBBY\aaaadBffdfffffhhhhhhegghfhhhd`^Bd__`_bbfffhdfdfegaggdaddadddfffcdccfcddd_a]aaaa
+@HWUSI-EAS163FR:13:1:13:13717:21119:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCTGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:13:13717:21119:0:1:1
+ggggggggegegggfgggagdgbdgebdfc[fddaddd_dba`aJ^\\]^dfcaddde`c]ab]bd`dd`_cccbaY]_]WTZT]\\\_XY]R]VZUZ\L_
+@HWUSI-EAS163FR:13:1:13:13717:21119:0:3:1
+GNNNACTACCCNNNTATCTAANCCTGTTTGCTCCCCACGCTTTCGCANCTGAGCGTAAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:13:13717:21119:0:3:1
+`BBB_bbbbbbBBB\_aaa^cBddafffdehhghhhhhhfhhhffd\Bd`^``ddRSU\V[Z[Z[hhhhh_c[caeabdcefdaddddad`acdd
+@HWUSI-EAS163FR:13:1:13:2231:21246:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:2231:21246:0:1:1
+hhhhhhhhchhhghffhghhghhhhhhghgfgghdfghehdhghhabfffbhhhhfdffdcafffbfffbcfaffeehhegf]Wgacafaffc]a`_c`fQ
+@HWUSI-EAS163FR:13:1:13:2231:21246:0:3:1
+GNNNACTACCGNNNTATCTAATCCTGTNTGATACCCACACTTTCGAGNCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:2231:21246:0:3:1
+aBBBa_aa^aaBBB^\aaaaghhhhffBffeeeee_c_cdfdfffdcBeeffdefhh]Yc[W_ffhffdh[ffRafdcccghf_cfadfdW[cfW
+@HWUSI-EAS163FR:13:1:13:11172:21249:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATCGGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:13:11172:21249:0:1:1
+hhhhhhhhhhhhhhhhhhfhhhgghdghhdhhggehggfhfegfhhcdgfdfebddffdfdaddfdfdfdcddcec`ccca_`__`aaa^ada___]a^aY
+@HWUSI-EAS163FR:13:1:13:11172:21249:0:3:1
+GNNNACTACACNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGNCTCAGCGTCAGTTTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:13:11172:21249:0:3:1
+_BBBZaaaaaaBBBZ^aaaahhhhhhhhhhhhhhhhhfghhhhhhb`Bbdbbdbdghdhhfffbfhffdhggdadcffffhbgad__]c[_c_aa
+@HWUSI-EAS163FR:13:1:13:1874:21266:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGCAAGTTT
++HWUSI-EAS163FR:13:1:13:1874:21266:0:1:1
+gggggggfgggggggggcggaggggfdffafeffdfafff_fedfdK`ddQfcfdfafc```fbd]dQ[_]f_fffabfaddbaf^``bbacf_J]_bW`e
+@HWUSI-EAS163FR:13:1:13:1874:21266:0:3:1
+GNNNACTACCGNNNTATCTAATCCTGTNTGATACCCACACTTTCGAGNCTCAATGTCAGTTGCAGCTCAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:1874:21266:0:3:1
+aBBB`^aa\aaBBBV[a\a\fhdafedBda]^acdfhfhhcafcfWaB_ca`^d_fcfffLb]LW`eJa_Sa^Ra^Wa]eLaaR^`[^daLKSa[
+@HWUSI-EAS163FR:13:1:13:3728:21370:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:3728:21370:0:1:1
+hhhhhhhhhhghhhhhhhhhhhhhhfcffdhhhhehhhhhhhghhfaffcbffcffcffa`_ddd_f`f``d_bdebfedff]_f`__bbaccc_^Y`Z_`
+@HWUSI-EAS163FR:13:1:13:3728:21370:0:3:1
+GNNNACNACGGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGNCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:3728:21370:0:3:1
+bBBB^\Ba^_\BBBZ[a\a\hhhhhhhhhfhgghhfhdhgfffff`dBbdbdbddhghghfdgdgeghfgfhhhgha]aghfefdbddddRa^a`
+@HWUSI-EAS163FR:13:1:13:14734:21363:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:13:14734:21363:0:1:1
+hhhhhhhhghhhhhhhhhfhhhhhhehhhchhffdhhgfhhghhhhffdhfffgfcfgdghfffhfggghbfd_fca_b_b]b_b_aabafccccdcabca
+@HWUSI-EAS163FR:13:1:13:14734:21363:0:3:1
+GNNNACTACGGNNNTATCTAANCCCGTTCGCTCCCCTGGCTTTCGCGNCTCAGCGTCAGTTTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:13:14734:21363:0:3:1
+^BBBYa`_aabBBB\aaaaaeBeeeedeeehhhhhhhhhgfhhhcd`Bd`d`addghdhdghhhgfghghehh_^aacfcdd[egcdcca^aaad
+@HWUSI-EAS163FR:13:1:13:2725:21428:0:1:1
+GTGTGCCAGNAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTCTGCAAGTCTGGAGTGAAAGCCC
++HWUSI-EAS163FR:13:1:13:2725:21428:0:1:1
+hhhhhfffeBdffffffheffffffhhhhhhgghhhhhghdhfhhh_hhhfghhffbfddacfcdbfdfdWf]cfghhgghedWcddffdWfddJ\W^^BB
+@HWUSI-EAS163FR:13:1:13:2725:21428:0:3:1
+GNNNACNACGCNNNTATCTAATCCCGTNCGCTCCCCTGGCTTTCGCGNCTCAGCGTCAGTTTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:13:2725:21428:0:3:1
+aBBB_`Bbba`BBBY^bba`hhhhhffBec^cccc\Jdccehhh[daB`adbddehehhhhhhcgeehhhcJ^[_bWWbbhagfcddbae[_fWd
+@HWUSI-EAS163FR:13:1:13:6824:21459:0:1:1
+NTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTCATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:13:6824:21459:0:1:1
+BSSSSWWWWWb__b___________VUVTTVVVVVYYYYY_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@HWUSI-EAS163FR:13:1:13:6824:21459:0:3:1
+GNNNACTACGCNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGNATCAGCGTCAGTTACAGTCCAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:13:6824:21459:0:3:1
+^BBBT\a]\_\BBB[W_W_Wfhhhhghhhg_ghhhhchhghhhgh^`B_`bb`_`ecfgfhffdfaffdfcfdfddddcfddd`cabaab\a\a_
+@HWUSI-EAS163FR:13:1:13:9876:21486:0:1:1
+NTGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:13:9876:21486:0:1:1
+BSSSSWVVVVb_bb__bbbbbbb__YYYYQPWWWW[Y[[[b_b__b__b________bb______________Z______WQQWVOUUUSYYYYPWWTWW_
+@HWUSI-EAS163FR:13:1:13:9876:21486:0:3:1
+GNNNACTACGCNNNTATCTAANCCTGTCTGCTCCCCACGCTTTCGCANCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:13:9876:21486:0:3:1
+`BBB_`bb`b`BBB\\a^_^dBddd]YF[[ZZ[[[gghgehhhfgbbBbb_bb`bdgdfdgggegfhhdhcddbcefdfffcfdddfcba[_aaa
+@HWUSI-EAS163FR:13:1:13:7294:21566:0:1:0
+NNGTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATCATTGGGCGTAAAGCGCGCGCAGGCGGATCGGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:13:7294:21566:0:1:0
+BBKOJNQNQQ__________YYYYYYYYYYVTTVV[[[[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@HWUSI-EAS163FR:13:1:13:7294:21566:0:3:0
+GNNNACNACCGNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGNCTCAGCGTCAGTTTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:13:7294:21566:0:3:0
+aBBB]_Baaa^BBBTX]V][hhhheghhgh_hghhhehghhhheha`B`ab_b`bddRfehhhefgfffaf[fgdcgfdffca_a_acca_d_d_
+@HWUSI-EAS163FR:13:1:14:4037:1434:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGAGTTATCCGGATTTAGTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:4037:1434:0:1:1
+hhhghhhhhhhhhhhhhhfghhgghedhhaadddb`Q`_bacaccgcdggYHa^^ZW[ZXaaccd`bbda^a\aad__b_aa__aaa`d`ddad`_]b]aa
+@HWUSI-EAS163FR:13:1:14:4037:1434:0:3:1
+GNNNACTACCCNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTNGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:14:4037:1434:0:3:1
+PBBBX`_aaabBBB`]``__ghhhghhhhhfhfhhhahhhhhhhhehhhhhhhhebfdedBdfbda_a_ahhcfgfhhhhhh]ghchhdddccge
+@HWUSI-EAS163FR:13:1:14:18004:1460:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:14:18004:1460:0:1:1
+hhhhhhhhhhfhhhhhhhfhhghhgfbffcQdbbbfdfdfddbddhddgghchhggchddbbd_fabdddddbag__aaa^\Y^`_a_aG^_Z_Y^a__^b
+@HWUSI-EAS163FR:13:1:14:18004:1460:0:3:1
+GNNNACTACAGNNNTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTTAGCGTCAGTNTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:14:18004:1460:0:3:1
+_BBB_aaaaaaBBBZ_____hhhhhhhhhhhhhhhhchghhhhfhd]hhdbhdfhbbbb`B_`^aZ\\\Ybbdddcdegf]ccda]^_^^U[^^_
+@HWUSI-EAS163FR:13:1:14:10965:1570:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTCATCCGGAATTACTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCC
++HWUSI-EAS163FR:13:1:14:10965:1570:0:1:1
+gggggggggggggggggggggggggddfffaffcfaN_][TPQQUURSXZ[F^\\ZUZZZaadddddae`a[aabc`aaZ_aa_aa_aaVW___WZSROYX
+@HWUSI-EAS163FR:13:1:14:10965:1570:0:3:1
+GNNNACTACGCNNNTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTNACGGCCCAGAGACCTGCCTTCGCCATTGGTGTTC
++HWUSI-EAS163FR:13:1:14:10965:1570:0:3:1
+^BBBVa]__Z]BBBX\]]_`hffhdafffcgghhhh`hhfghhdhhdhhgefeef^aa`_Bbb__``a^_aabae_adgaacaccZR\\\R][^^
+@HWUSI-EAS163FR:13:1:14:6225:1638:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTAGTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:14:6225:1638:0:1:1
+ggggggggggggggfgggggggggggeggg`gggg]O^[^bb`dbggfggWMZZU_`b_`gdfggdQbdddgaddaad__bbb_]_baaa]UZ_`aadabf
+@HWUSI-EAS163FR:13:1:14:6225:1638:0:3:1
+GNNNACTACGCNNNTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTNTTCGTCCAGGGGGCCGCCTTCGCCACAGGTATTC
++HWUSI-EAS163FR:13:1:14:6225:1638:0:3:1
+aBBBabbbbb]BBBY]___]hhhhhhhhhhhhhhhhfhghhhhhfhhhhhdechgbdbbbBZ^^]bddb`_gggghcddacfaaf`b`[_[`^[_
+@HWUSI-EAS163FR:13:1:14:19237:1628:0:1:1
+GTGTGCNAGCCGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:19237:1628:0:1:1
+hhhhhfBfffdfffdhhhghhhhhhgghhaacfccghhghdhhhhgcehhchhhgfadedcdgdgbeeeabd_bdgcdcabdbaaabadadddda__daaa
+@HWUSI-EAS163FR:13:1:14:19237:1628:0:3:1
+GNNNACTACAGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTNGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:14:19237:1628:0:3:1
+aBBB^aaaaa_BBB[^aaaahhhhhhhhghghghhhghghhhhhghhhhhhhahh`bbb`B^a^a]\\\\fgdadcadegde[gbdaac_Wdada
+@HWUSI-EAS163FR:13:1:14:12932:1741:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAGATCCC
++HWUSI-EAS163FR:13:1:14:12932:1741:0:1:1
+hhghhhhhhhhhhhhhghhhhhhhhhghhgbffffdhfehhgghggghhhbUb```bd`bggghhhffghffffgfdhfdebe_daddaaddaa___Q`]c
+@HWUSI-EAS163FR:13:1:14:12932:1741:0:3:1
+GNNNACTACCGNNNTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTNTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:14:12932:1741:0:3:1
+^BBB\aaaaaaBBB^`````hghhh^fffffdhhhhghhgghhgahhfhfggghh`daa^Bddddbdb`bda_ehhhfhg_fW_d\d^`Z\aaaa
+@HWUSI-EAS163FR:13:1:14:12140:1797:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:14:12140:1797:0:1:1
+hhhhhhhhhhhhhhhhhhghhhhhh`bff]bdbbbhghghggehhhdahh^Ra`^```^`dfffgaedebahddfd___]____a`cada_bbI___aa_]
+@HWUSI-EAS163FR:13:1:14:12140:1797:0:3:1
+GNNNACTACACNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGCCTCAGCGTCAGTNTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:14:12140:1797:0:3:1
+aBBB_aaaaa]BBBX\`\`_hhhhchhhhehhhhhf`affhhhhchchhhhhghgbfddbBddddbdddbgghgahghhdhhhgh_dbdc_daad
+@HWUSI-EAS163FR:13:1:14:9185:1953:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGCGCGCGCAGGCGGATCGGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:14:9185:1953:0:1:1
+hhhghhhhhhhhhhhhhhghhhhhhdhhhdhghhgcWfccfdffdddfhhbR`_```b`bhfdfggfgfhfhddfcf_fcaac_c\aa_\cabacaaa``b
+@HWUSI-EAS163FR:13:1:14:9185:1953:0:3:1
+GNNNACTACCGNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGCCTCAGCGTCAGTNTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:14:9185:1953:0:3:1
+^BBB]aa^^\^BBBXbbbb`hhhhhhhhhfhfhhhhchhhfhhhhhhhgcfdfffbfffdBeeed`eeedheccghghhhhhghhghhgRacacf
+@HWUSI-EAS163FR:13:1:14:9209:1945:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGCGCGCAGGTGGATGTGTAAGTCTGTTTTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:9209:1945:0:1:1
+ffffaffffed_ddfafffa`d_`dQU]ZTKRQKP^M]\^W_Z^_[PH^\SEZTUTKPWOZW^H^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@HWUSI-EAS163FR:13:1:14:9209:1945:0:3:1
+GNNNACTACCGNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGCCTCAGCGTCAGTNTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:14:9209:1945:0:3:1
+_BBB]aaaaa\BBB]Z__]_ffff[fffLfcffffccfffffffadfaafacaWa`^Y``B`^I]WQNWYJ^^^\W^`\efffc``[b^bPJW_^
+@HWUSI-EAS163FR:13:1:14:5635:2015:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTACTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCC
++HWUSI-EAS163FR:13:1:14:5635:2015:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhghhhh]ffcfaOcabfffffhfghh`Hdd`aaa_agghfhhfhhfeghghgdfgfaddbdddgbg_dccaccdabf
+@HWUSI-EAS163FR:13:1:14:5635:2015:0:3:1
+GNNNACTACGCNNNTATCTAATCCTGTTCGCTCCCTACGCTTTCGCTCCTCAGCGTCAGTNACGGCCCAGAGACCTGCCTTCGCCATTGGTGTTC
++HWUSI-EAS163FR:13:1:14:5635:2015:0:3:1
+aBBB`aaaaa\BBBTa``_YhhhhghhhhhhghhhdcfhghhhhhhfhhhhhhhhfffffBddd`ddd``feefeddffdhhgeheeggdad_de
+@HWUSI-EAS163FR:13:1:14:17418:2043:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:17418:2043:0:1:1
+hhhhhhhhhhhhhhhhhhghhhhhhhfhhfghhhegghghhgfhggdhhhcghggdafedddgedcgfgdcg[dggbcdebddadcedddeeagaaac\bd
+@HWUSI-EAS163FR:13:1:14:17418:2043:0:3:1
+GNNNACTACAGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTNGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:14:17418:2043:0:3:1
+aBBBaaaaaaZBBBW^aaaahhhhhhhhhhdchhhhhhhhhhhhghhghhhhchhfffffBdebd^[\[[[fddfhggggfghegeggLe]dab_
+@HWUSI-EAS163FR:13:1:14:16008:2079:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:14:16008:2079:0:1:1
+hhhhhhhhhhhhhhhghhhhhhhhhfdffc`ffffhgfehgcghhfe[hheehea]afccffhcgecbecdhffgdedgda``accdbdQ_aac\`]`_^c
+@HWUSI-EAS163FR:13:1:14:16008:2079:0:3:1
+GNNNACTACCGNNNTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTNTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:14:16008:2079:0:3:1
+^BBB[]a_a]aBBB\`b`bahhhhhfghhhhhhhhhchhghhhhhhWhhhfhgggbbbbbB`d`d___[_]ddcdeedfffdacfddcdda[daa
+@HWUSI-EAS163FR:13:1:14:14760:2094:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:14760:2094:0:1:1
+hhhhhhhhhhhhhhghhghhhhhhhhghhdhghhchhhhhfhgghfcfffdhhhcfaffabcdedahdhgbf_dedaaeddedaedccedfffg]aagdde
+@HWUSI-EAS163FR:13:1:14:14760:2094:0:3:1
+GNNNACTACGGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTNGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:14:14760:2094:0:3:1
+^BBBW_aa__`BBB]\a^a_hhhhhhhhhhghhhhhhhhhhhhhhhhhhhhhghgaffccB``^`JTWWWfhdfffchhffhbgeddgdacdcab
+@HWUSI-EAS163FR:13:1:14:8199:2240:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTTTAAAGGGCGCGCAGGCGGATCTGTCAGTCTGTCTTGAAAGTTC
++HWUSI-EAS163FR:13:1:14:8199:2240:0:1:1
+hhhhhhhhhhhghhhhgghhhhhhhR[a_OROWPU^Q^]^Zda`ab^KbbZK\ZZTILTT^^`K`Z`^`QZ[JJ[ZZZOFITFQR___a`BBBBBBBBBBB
+@HWUSI-EAS163FR:13:1:14:8199:2240:0:3:1
+GNNNACTACGGNNNTATCTAATCCCGTTTGCTCCCCTGGCTTTCGCGCCTCAGCGTCAGTNTTCGTCCAGAAAGCCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:14:8199:2240:0:3:1
+^BBBWaa___IBBBT\aaaahhhh]fffQfLd[ee^KLY^ededa[fffffcR[f]^^^^BUUT[OKNXUN]Z\L\[a`^dhdd[WQQ[[R^^__
+@HWUSI-EAS163FR:13:1:14:10159:2240:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGTGTTATCCGGATTTACTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:10159:2240:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhbFdbbcffffgfhhh^Hc_^_^_a_hfghhfghhg`[_`bhgggdggcegchhgdegaeccdgdaf
+@HWUSI-EAS163FR:13:1:14:10159:2240:0:3:1
+GNNNACTACGGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTNGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:14:10159:2240:0:3:1
+^BBB]a_a___BBBZaaa_ahhhhhhhhhghhfhhghhhhhhhghhghhfhhhdh_`d``B`e``a^^^_dhddhcbgggegdgfb`L_^]a_ac
+@HWUSI-EAS163FR:13:1:14:19702:2247:0:1:1
+GTGTGCNAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:14:19702:2247:0:1:1
+fffffdBdddY\aa^fffdffffffdfffcfffffeffeffefffecdefeeededffdeedddeeeddededdddddYY`]U]`_cccadddabbac`c_
+@HWUSI-EAS163FR:13:1:14:19702:2247:0:3:1
+GNNNACTACGGNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGCCTCAGCGTCAGTATTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:14:19702:2247:0:3:1
+^BBB]aaaaabBBB\Z_\\_hgghhhhhhcfchhhhccghhhhghhhhhhhahhfefhfaRfdbdeffefhhhhahghegefeccccccaZ^]``
+@HWUSI-EAS163FR:13:1:14:10956:2321:0:1:1
+GTGTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATCAGTCAGTCTCTCTTAAAAGTTC
++HWUSI-EAS163FR:13:1:14:10956:2321:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhaafefhhhhhhhhhhdFdb``dd^ddhehhhhhghd[dcdeeaheeaedeOVFFEVTNNSgfge`g
+@HWUSI-EAS163FR:13:1:14:10956:2321:0:3:1
+GNNNACTACCCNNNTATCTAATCCCGTTCGCTCCCCTGGCTTTCGCGCCTCAGCGTCAGTNTTCGTCCAGAAAGTCGCCTTCGCCACTGGTGTTC
++HWUSI-EAS163FR:13:1:14:10956:2321:0:3:1
+^BBB]aaaaaaBBBZaaaaahhhhhhhhhcfdffffcfffhhhhghahheffefe^da`^Ba`d``dfbbghhecfafeadebdfac_a_M^\Z^
+@HWUSI-EAS163FR:13:1:14:14947:2338:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCC
++HWUSI-EAS163FR:13:1:14:14947:2338:0:1:1
+hhhhhhhhhhhhhhhhhhghghhhhhehhhbffdfffhhhhegghhhdhhgegaehhadcgggghgfghg[e_aegdfbdcdedc]dcc[_c_caW\Z^^h
+@HWUSI-EAS163FR:13:1:14:14947:2338:0:3:1
+GNNNACTACCGNNNTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTC
++HWUSI-EAS163FR:13:1:14:14947:2338:0:3:1
+`BBB`bbbb`^BBB[``___hhhhhhhhhhhhhhhhghhhhhhhghahhg]fcffdfff]ZQ^]`ghehfgbgggddehcegccgdfd]bVaa_c
+@HWUSI-EAS163FR:13:1:14:3515:2423:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:3515:2423:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhfaffZ`bbbbhfhghhhghhhbhhh_N__da^da^dbfeeafcfeaf_achadddddcaeddbgacede__adbbc
+@HWUSI-EAS163FR:13:1:14:3515:2423:0:3:1
+GNNNACTACACNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTNGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:14:3515:2423:0:3:1
+_BBBZ_aa_\\BBBW]````hhhhhghhhhchahhhgh[hhhhhh_hhhhhhg_hdddddB[aWaaa_a^caacfddffdhhhgJbb`^_abccd
+@HWUSI-EAS163FR:13:1:14:6115:2415:0:1:1
+GTGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTACTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTT
++HWUSI-EAS163FR:13:1:14:6115:2415:0:1:1
+hhhhhhhhhhhhhhhhhhhhhhhhhhdhh[Zadaa\F\Z\`dda`hehhh`Mda`a^^a_hghhgahhhfghaahgdfgfadgegdfag`fhfg__dda_a
+@HWUSI-EAS163FR:13:1:14:6115:2415:0:3:1
+GNNNACTACGGNNNTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTNGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTC
++HWUSI-EAS163FR:13:1:14:6115:2415:0:3:1
+aBBB_a`aa]ZBBBYaaaaahhhhhhhhhhdhchhhhhhhhhhhghhhghehhghbdfdbB`ead`\\^^fhdefacffadfddWb`b``adabe

data/spec/trimmer_spec.rb

@@ -0,0 +1,47 @@
+require 'spec_helper'
+
+describe Lederhosen::Trimmer do
+
+  describe Lederhosen::Trimmer::PairedTrimmer do
+
+  end
+
+  describe Lederhosen::Trimmer::QSEQTrimmer do
+
+    let(:qseq_trimmer) { Lederhosen::Trimmer::QSEQTrimmer.new 'spec/data/ILT_L_9_B_001_1.txt.gz', 'spec/data/ILT_L_9_B_001_3.txt.gz' }
+
+    it 'can be initialized' do
+      qseq_trimmer.should_not be_nil
+    end
+
+    it 'has an #each function that generates record objects' do 
+      qseq_trimmer.each do |x|
+        x.should be_an_instance_of Fasta
+      end
+    end
+
+    it 'should create an even number of records (not output singletons)' do
+      qseq_trimmer.to_a.flatten.size.should be_even
+    end
+  end
+
+  describe Lederhosen::Trimmer::InterleavedTrimmer do
+
+    let(:interleaved_trimmer) { Lederhosen::Trimmer::InterleavedTrimmer.new 'spec/data/example.fastq' }
+
+    it 'can be initialized' do
+      interleaved_trimmer.should_not be_nil
+    end
+
+    it 'has an #each function that generates record objects' do 
+      interleaved_trimmer.each do |x|
+        x.should be_an_instance_of Fasta
+      end
+    end
+
+    it 'should create an even number of records (not output singletons)' do
+      interleaved_trimmer.to_a.flatten.size.should be_even
+    end
+  end
+
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.4.0
+  version: 1.6.0
   prerelease: 
 platform: ruby
 authors:
@@ -18,7 +18,7 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.0.12
+        version: 0.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.0.12
+        version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: progressbar
   requirement: !ruby/object:Gem::Requirement
@@ -150,6 +150,7 @@ files:
 - lib/lederhosen/tasks/split_fasta.rb
 - lib/lederhosen/tasks/trim.rb
 - lib/lederhosen/tasks/version.rb
+- lib/lederhosen/trimmer.rb
 - lib/lederhosen/version.rb
 - readme.md
 - spec/cli_spec.rb
@@ -157,10 +158,11 @@ files:
 - spec/data/ILT_L_9_B_001_3.txt.gz
 - spec/data/ILT_L_9_B_002_1.txt.gz
 - spec/data/ILT_L_9_B_002_3.txt.gz
+- spec/data/example.fastq
 - spec/data/test.uc
-- spec/misc_spec.rb
 - spec/no_tasks_spec.rb
 - spec/spec_helper.rb
+- spec/trimmer_spec.rb
 homepage: http://audy.github.com/lederhosen
 licenses:
 - MIT
@@ -176,7 +178,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 598176715743028608
+      hash: 2684834348311279261
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/spec/misc_spec.rb

@@ -1,11 +0,0 @@
-require 'spec_helper'
-
-describe String do
-  it 'generate_kmers should generate kmers for a string' do
-    'test'.to_kmers(2).should == ['te', 'es', 'st']
-    'test'.to_kmers(3).should == ['tes', 'est']
-    'test'.to_kmers(4).should == ['test']
-    'test'.to_kmers(5).should == []
-    'test'.to_kmers(0).should == []
-  end
-end