nugen_barcode_splitter 0.0.1

data/bin/base_adder

@@ -0,0 +1,22 @@
+#!/usr/bin/env ruby
+require "nugen_barcode_splitter"
+
+usage =<<EOF
+  #{$0} file.fq number_of_bases out.fq
+
+  -_-_-_-_- #{$0} -_-_-_-_-
+
+  Adds N^P bases to the beginning of the
+  fastq file. The Quality is set on the
+  lowest value.
+EOF
+
+file_dir = ARGV[0]
+number_of_bases = ARGV[1].to_i
+out_dir = ARGV[2]
+
+fastq = Fastq.new("file_dir")
+fastq.add(number_of_bases, out_dir)
+fastq.close
+
+

data/bin/nugen_barcode_splitter

@@ -0,0 +1,156 @@
+#!/usr/bin/env ruby
+require "rubygems"
+require "yaml"
+require "optparse"
+
+usage =<<EOF
+      #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
+_____________________________________________________________________________
+
+      Example sample_sheet_nugen.csv :
+
+FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
+C0ED3ACXX,4,S1,hg19,ACCC,RNA Seq,N,,,33333
+C0ED3ACXX,4,S2,hg19,GAGT,RNA Seq,N,,,44444
+C0ED3ACXX,4,S3,hg19,CGTA,RNA Seq,N,,,33333
+C0ED3ACXX,4,S4,hg19,TTAG,RNA Seq,N,,,44444
+C0ED3ACXX,5,S5,hg19,AGGG,RNA Seq,N,,,33333
+C0ED3ACXX,5,S6,hg19,GTCA,RNA Seq,N,,,44444
+C0ED3ACXX,6,S7,hg19,CCAT,RNA Seq,N,,,33333
+
+      Note: The sample names must be alphanumerical!
+_____________________________________________________________________________
+
+EOF
+
+options = {
+  :project_dir => nil,
+  :out_dir => nil,
+  :sample_sheet => nil,
+  :eol_only? => "",
+  :bel_only? => "",
+  :mismatches => "",
+  :keep_barcode => "",
+  :fastq_multx => "fastq_multx",
+  :debug => false
+}
+
+optparse = OptionParser.new do |opts|
+  opts.banner = usage
+
+  opts.on("-p", "--project_dir", :REQUIRED, String,
+    "Illumina project directory (../Unaligned/ProjectXXX/)") do |i|
+    options[:project_dir] = i if i
+  end
+
+  opts.on("-o", "--out_dir", :REQUIRED, String,
+    "The desired output directory") do |i|
+    options[:out_dir] = i if i
+  end
+
+  opts.on("-s","--sample_sheet", :REQUIRED, String,
+    "Please provide your sample_sheet") do |i|
+    options[:sample_sheet] = i if i
+  end
+
+  opts.on("-e","--end_of_line",
+    "Limit the search for the barcode to the end of the line DEFAULT:false") do |i|
+    options[:eol_only?] = "-e"
+  end
+
+  opts.on("-b","--begin_of_line",
+    "Limit the search for the barcode to the start of the line DEFAULT:false") do |i|
+    options[:bol_only?] = "-b"
+  end
+
+  opts.on("-k","--keep_barcode",
+    "Do not trim of the barcode DEFAULT:false") do |i|
+    options[:keep_barcode] = "-x"
+  end
+
+  opts.on("-m","--mismatches NUM", Integer, "Number of mismatches (Default:1)") do |i|
+    options[:mismatches] = "-m #{i}" if i
+  end
+
+  opts.on("-x", "--fastq_multx DIR", String) do |i|
+    options[:fastq_multx] = i if i
+  end
+
+  opts.on("-d", "--debug", "Debug mode!") do |i|
+    options[:debug] = true
+  end
+
+  opts.on_tail("-h", "--help", "Show this message") do
+    puts opts
+    exit
+  end
+end
+
+begin
+  optparse.parse!
+  mandatory = [:project_dir, :out_dir, :sample_sheet]
+  missing = mandatory.select{ |param| options[param].nil? }
+  if !missing.empty?
+    puts "\nMissing options given or missing in config_file: \n\t#{missing.join(",\n\t")}"
+    puts optparse
+    exit
+  end
+rescue OptionParser::InvalidOption, OptionParser::MissingArgument
+   puts $!.to_s
+   puts optparse
+   exit
+end
+
+STDERR.puts "CURRENT OPTIONS:"
+STDERR.puts options.to_yaml
+
+# Read out sample_sheet
+sample_sheet = SampleSheet.new(options[:sample_sheet])
+sample_sheet.create_barcode_txt("#{options[:out_dir]}/barcode")
+
+# Prepare template
+multx_opts = "#{options[:keep_barcode]} #{options[:eol_only]} #{options[:bol_only]} #{options[:mismatches]}"
+nugen_temp = NugenTemplate.new(options[:fastq_multx],multx_opts)
+
+Dir.glob(options[:project_dir]).each do |p|
+  next unless File.directory? p
+  next unless p =~ /Sample_Lane/
+  outdir = ""
+
+  Dir.glob(p).each do |fwd|
+    next if File.directory fwd
+    next unless fwd =~ /Lane[1-8]_NoIndex_L[0-9]{3}_R1_[0-9]{3}.fastq.gz/
+    rev = fwd.gsub(/_R1_/, "_R2_")
+    tmp = fwd.split("/")
+    tmp = tmp[-1].split("_")
+    lane = tmp[0].qsub(/\D/,"")
+    number = tmp[4].qsub(/\D/,"")
+    barcodes = "#{options[:out_dir]}/barcode_#{lane}.txt"
+    outdir = options[:outdir] + "/Lane#{lane}"
+    begin
+      FileUtils.mkdir_p outdir unless File.directory? outdir
+    rescue Exception => e
+      STDERR.puts e.message
+    end
+    cmd = nugen_temp.fill(lane,number,outdir, barcodes, fwd, rev)
+    if options[:debug]
+      puts cmd if options[:debug]
+    else
+      status = system(cmd)
+      raise "Calling the template did not succeed!" if !status
+    end
+  end
+
+  # Add the trimmed bases
+  Dir.glob(outdir).each do |fwd|
+    next unless fwd =~ /R1_[0-9]{3}./
+    cmd = `base_adder #{fwd} 4 #{fwd}_added`
+    if options[:debug]
+      puts cmd if options[:debug]
+    else
+      status = system(cmd)
+      raise "Calling the template did not succeed!" if !status
+    end
+  end
+
+end

data/lib/nugen_barcode_splitter/fastq.rb

@@ -0,0 +1,26 @@
+class Fastq
+  def initialize(filename)
+    @filehandle = File.open(filename, "r")
+    line = @filehandle.readline()
+    raise RuntimeError, "Invalid fastq file!" if !line.include?("@")
+    @filehandle.pos = 0
+  end
+
+  def add(num, outdir)
+    bases = "N" * num
+    qualities = "@" * num
+    outfile = File.open(outdir, 'w')
+
+    while !@filehandle.eof?
+      outfile.write(@filehandle.readline)
+      outfile.write("#{bases}" + @filehandle.readline)
+      outfile.write(@filehandle.readline)
+      outfile.write("#{qualities}" + @filehandle.readline)
+    end
+    outfile.close()
+  end
+
+  def close()
+    @filehandle.close()
+  end
+end

data/lib/nugen_barcode_splitter/nugen_template.rb

@@ -0,0 +1,42 @@
+require "erubis"
+
+class NugenTemplate
+
+  def initialize(fastq_multx, options)
+    @template =<<EOF
+
+    #!/bin/bash
+    #\$ -pe DJ 4
+    #\$ -l h_vmem=6G
+    #\$ -j y
+    #\$ -N fq.Lane<%= @lane %>.<%= @number %>
+    #\$ -o <%= @lane_dir %>/nugen_demultiplexing.log
+
+    #{fastq_multx} #{options} -B <%= @barcodes %> \\
+      <(gunzip -c <%= @fwd %>) <(gunzip -c <%= @rev %>) \\
+      -o <%= @lane_dir %>/<%= @r1 %>.%.fq <%= @lane_dir %>/<%= @r2 %>.%.fq
+EOF
+  end
+
+  def fill(lane, number, lane_dir, barcodes, fwd, rev)
+
+    context = {
+      :lane => lane,
+      :number => number,
+      :lane_dir => lane_dir,
+      :barcodes => barcodes,
+      :fwd => fwd,
+      :rev => rev,
+      :r1 => "R1_#{number}",
+      :r2 => "R2_#{number}"
+    }
+
+    eruby = Erubis::Eruby.new(@template)
+    eruby.evaluate(context)
+  end
+
+  def to_s
+    template = "#{@template.chomp()}"
+  end
+
+end

data/lib/nugen_barcode_splitter/sample_sheet.rb

@@ -0,0 +1,41 @@
+require "csv"
+
+# Samplesheets are suppose to look like this
+=begin
+FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject,
+C0ED3ACXX,4,R-1,hg19,ACCC,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,4,R-2,hg19,GAGT,RNA Seq,N,,,47644,Nugen barcodes
+=end
+
+class SampleSheet
+
+  def initialize(samplesheet)
+    @lanes = []
+    @sample_id = []
+    @barcodes = []
+
+    CSV.foreach(samplesheet, {:headers => :first_row}) do |row|
+      @lanes << row["Lane"]
+      @sample_id << row["SampleID"].gsub(/\W/,"X")
+      @barcodes << row["Index"]
+    end
+  end
+
+  attr_accessor :lanes, :sample_id, :barcodes
+
+  def create_barcode_txt(prefix)
+    current_lane = "dummy"
+    handler = File.new(prefix,'w')
+    @lanes.each_with_index do |lane, i|
+      if current_lane != lane
+        outfile = "#{prefix}_#{lane}.txt"
+        current_lane = lane
+        handler = File.new(outfile,'w')
+        handler.write("# SampleName Barcode \n")
+      end
+      handler.write("#{@sample_id[i]} #{@barcodes[i]} \n")
+    end
+    File.delete(prefix)
+  end
+
+end

data/lib/nugen_barcode_splitter/statistics.rb

@@ -0,0 +1,37 @@
+class Statistics
+
+  def initialize(lane_log, barcodes)
+    @num_reads = Array.new(barcodes.length(),0)
+    @num_unmatched = 0
+    @total = 0
+    @barcodes = barcodes
+    File.open(lane_log).each do |line|
+      next if line.include?("Id")
+      next if line.empty?
+      line = line.split("\t")
+      case line[0]
+      when "unmatched"
+        @num_unmatched += line[1].to_i
+      when "total"
+        @total += line[1].to_i
+      else
+        if i = @barcodes.index(line[0])
+          @num_reads[i]+= line[1].to_i
+        end
+      end
+    end
+  end
+
+  attr_accessor :num_reads, :num_unmatched, :total, :barcodes
+
+  def to_s
+    str = "Statistics: \nBarcode\t# of reads\n"
+    @barcodes.each_with_index do |code, i|
+      str += "#{code}:\t#{@num_reads[i]} \n"
+    end
+    percent = (100 / @total.to_f) * @num_unmatched.to_f
+    percent = (percent.to_f * 100).round / 100.to_f
+    str += "Unmatched:\t#{@num_unmatched}\t(#{percent.to_f}%)\n"
+    str += "Total:\t#{@total}"
+  end
+end

data/lib/nugen_barcode_splitter.rb

@@ -0,0 +1,10 @@
+require "nugen_barcode_splitter/nugen_template"
+require "nugen_barcode_splitter/fastq"
+require "nugen_barcode_splitter/sample_sheet"
+require "nugen_barcode_splitter/statistics"
+
+class NugenBarcodeSplitter
+
+end
+
+

data/test/fixtures/Lane4.log

@@ -0,0 +1,56 @@
+Id	Count	File(s)
+R1	1063349	nugen/R1_001.R1.fq	nugen/R2_001.R1.fq
+R2	1002895	nugen/R1_001.R2.fq	nugen/R2_001.R2.fq
+R12	809924	nugen/R1_001.R12.fq	nugen/R2_001.R12.fq
+R22	933773	nugen/R1_001.R22.fq	nugen/R2_001.R22.fq
+unmatched	180059	nugen/R1_001.unmatched.fq	nugen/R2_001.unmatched.fq
+total	3990000
+Id	Count	File(s)
+R1	1046860	nugen/R1_002.R1.fq	nugen/R2_002.R1.fq
+R2	996545	nugen/R1_002.R2.fq	nugen/R2_002.R2.fq
+R12	807472	nugen/R1_002.R12.fq	nugen/R2_002.R12.fq
+R22	831454	nugen/R1_002.R22.fq	nugen/R2_002.R22.fq
+unmatched	307669	nugen/R1_002.unmatched.fq	nugen/R2_002.unmatched.fq
+total	3990000
+Id	Count	File(s)
+R1	1086329	nugen/R1_003.R1.fq	nugen/R2_003.R1.fq
+R2	951836	nugen/R1_003.R2.fq	nugen/R2_003.R2.fq
+R12	836954	nugen/R1_003.R12.fq	nugen/R2_003.R12.fq
+R22	895243	nugen/R1_003.R22.fq	nugen/R2_003.R22.fq
+unmatched	219638	nugen/R1_003.unmatched.fq	nugen/R2_003.unmatched.fq
+total	3990000
+Id	Count	File(s)
+R1	1083328	nugen/R1_004.R1.fq	nugen/R2_004.R1.fq
+R2	976776	nugen/R1_004.R2.fq	nugen/R2_004.R2.fq
+R12	827858	nugen/R1_004.R12.fq	nugen/R2_004.R12.fq
+R22	974454	nugen/R1_004.R22.fq	nugen/R2_004.R22.fq
+unmatched	127584	nugen/R1_004.unmatched.fq	nugen/R2_004.unmatched.fq
+total	3990000
+Id	Count	File(s)
+R1	1096656	nugen/R1_005.R1.fq	nugen/R2_005.R1.fq
+R2	867273	nugen/R1_005.R2.fq	nugen/R2_005.R2.fq
+R12	849238	nugen/R1_005.R12.fq	nugen/R2_005.R12.fq
+R22	858169	nugen/R1_005.R22.fq	nugen/R2_005.R22.fq
+unmatched	318664	nugen/R1_005.unmatched.fq	nugen/R2_005.unmatched.fq
+total	3990000
+Id	Count	File(s)
+R1	963137	nugen/R1_006.R1.fq	nugen/R2_006.R1.fq
+R2	738468	nugen/R1_006.R2.fq	nugen/R2_006.R2.fq
+R12	751315	nugen/R1_006.R12.fq	nugen/R2_006.R12.fq
+R22	817436	nugen/R1_006.R22.fq	nugen/R2_006.R22.fq
+unmatched	719644	nugen/R1_006.unmatched.fq	nugen/R2_006.unmatched.fq
+total	3990000
+Id	Count	File(s)
+R1	1037730	nugen/R1_007.R1.fq	nugen/R2_007.R1.fq
+R2	774785	nugen/R1_007.R2.fq	nugen/R2_007.R2.fq
+R12	800517	nugen/R1_007.R12.fq	nugen/R2_007.R12.fq
+R22	793770	nugen/R1_007.R22.fq	nugen/R2_007.R22.fq
+unmatched	583198	nugen/R1_007.unmatched.fq	nugen/R2_007.unmatched.fq
+total	3990000
+Id	Count	File(s)
+R1	1156538	nugen/R1_008.R1.fq	nugen/R2_008.R1.fq
+R2	919772	nugen/R1_008.R2.fq	nugen/R2_008.R2.fq
+R12	875997	nugen/R1_008.R12.fq	nugen/R2_008.R12.fq
+R22	879468	nugen/R1_008.R22.fq	nugen/R2_008.R22.fq
+unmatched	158225	nugen/R1_008.unmatched.fq	nugen/R2_008.unmatched.fq
+total	3990000

data/test/fixtures/barcode_4.txt

@@ -0,0 +1,5 @@
+# SampleName Barcode 
+RX1 ACCC 
+RX2 GAGT 
+RX1X2 CGTA 
+RX2X2 TTAG 

data/test/fixtures/barcode_5.txt

@@ -0,0 +1,5 @@
+# SampleName Barcode 
+RX3 AGGG 
+RX4 GTCA 
+RX3X2 CCAT 
+RX4X2 TATC 

data/test/fixtures/barcode_6.txt

@@ -0,0 +1,5 @@
+# SampleName Barcode 
+RX5 ACCC 
+RX6 GAGT 
+RX5X2 CGTA 
+RX6X2 TTAG 

data/test/fixtures/barcode_7.txt

@@ -0,0 +1,5 @@
+# SampleName Barcode 
+RX7 AGGG 
+RX8 GTCA 
+RX7X2 CCAT 
+RX8X2 TATC 

data/test/fixtures/barcode_8.txt

@@ -0,0 +1,5 @@
+# SampleName Barcode 
+RX9 ACCC 
+RX10 GAGT 
+RX9X2 CGTA 
+RX10X2 TTAG 

data/test/fixtures/invalid.fq

@@ -0,0 +1,20 @@
+>HWI-ST628:191:c0299abxx:1:1101:1010:2080 1:Y:0:CGATGT
+NGTANNCAAATCAAACACCTGACTCCNNNAANGAGCCNGNATTNTNTGANANNTNNNNNNANNNCTTNTGTNTTTAGAATAAGACAGCCTGTGGGAGTGT
++
+####################################################################################################
+>HWI-ST628:191:c0299abxx:1:1101:1030:2115 1:N:0:CGATGT
+TGCACAGACACACACACAAACACATGACGTGCATACACACACACTTGTATACAGACATAAACATACACACACATTTATACATGCATAAACACACACAAAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJIJJJHIJJJIIJJJJIJIJJJJHIJJJJJJJJJJIJHHHHHFFFFDDCDDDEFEDDDDDDDDDCDDDDDDDDDDD
+@HWI-ST628:191:c0299abxx:1:1101:1141:2140 1:N:0:CGATGT
+AGGTTTAAGTGAATATAAGAGCAACAATGACATGAACCAGCCAGGCTTTTGCTTGATGCTGTAATTCAGTGTTTGACCCTGCTGACATTTGTGTTGTCAG
++
+BBCDDFFFHHHHHJIJJJJIJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJJJJJJJJJJJJIJJJJJHHGIJIIHHHHHFFFFFEEEEEEECCDDDDC
+@HWI-ST628:191:c0299abxx:1:1101:1225:2144 1:N:0:CGATGT
+TACAATTATATTAGTATAAAAATGAGCAATTTTTAAAATGAGGCGTGGCATTAAACGTGGCTAATTCATACAAATTCCATATGATAATACTGGTATAAAA
++
+CCCFFFFFHHHHHJHIIJJJJJJJJJJJIJJJJJJIJJJJJJJJJIJJJJJJJJJJJHJJJJJJHHHHHHHFFFFFFEEEEEEDEDDDEDDED@CDEEEC
+@HWI-ST628:191:c0299abxx:1:1101:1036:2155 1:N:0:CGATGT
+TGTTCAGGCTTTTGTTTTAATCAGAGCCTTTTATTTTTAGGACTAATAACTCTGTCACCCCATTGTTTGGGTTTTTGATGGATGAATATTTTTATTTGGC
++
+@C@FDFFFHHFBHEHHIIIIIIDH>GGEHIGIIIIIIGBBG>BG@GIIIIIIIIGIHDGIGIHIIHHIIBE?EHHBBBCCDCDEBADDEDCDC<CCDC@>

data/test/fixtures/sample_sheet.csv

@@ -0,0 +1,21 @@
+FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject,
+C0ED3ACXX,4,R-1,hg19,ACCC,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,4,R-2,hg19,GAGT,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,4,R-1-2,hg19,CGTA,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,4,R-2-2,hg19,TTAG,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,5,R-3,hg19,AGGG,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,5,R-4,hg19,GTCA,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,5,R-3-2,hg19,CCAT,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,5,R-4-2,hg19,TATC,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,6,R-5,hg19,ACCC,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,6,R-6,hg19,GAGT,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,6,R-5-2,hg19,CGTA,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,6,R-6-2,hg19,TTAG,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,7,R-7,hg19,AGGG,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,7,R-8,hg19,GTCA,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,7,R-7-2,hg19,CCAT,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,7,R-8-2,hg19,TATC,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,8,R-9,hg19,ACCC,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,8,R-10,hg19,GAGT,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,8,R-9-2,hg19,CGTA,RNA Seq,N,,,47644,Nugen barcodes
+C0ED3ACXX,8,R-10-2,hg19,TTAG,RNA Seq,N,,,47644,Nugen barcodes

data/test/fixtures/test.fq

@@ -0,0 +1,20 @@
+@HWI-ST628:191:c0299abxx:1:1101:1010:2080 1:Y:0:CGATGT
+NGTANNCAAATCAAACACCTGACTCCNNNAANGAGCCNGNATTNTNTGANANNTNNNNNNANNNCTTNTGTNTTTAGAATAAGACAGCCTGTGGGAGTGT
++
+####################################################################################################
+@HWI-ST628:191:c0299abxx:1:1101:1030:2115 1:N:0:CGATGT
+TGCACAGACACACACACAAACACATGACGTGCATACACACACACTTGTATACAGACATAAACATACACACACATTTATACATGCATAAACACACACAAAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJIJJJHIJJJIIJJJJIJIJJJJHIJJJJJJJJJJIJHHHHHFFFFDDCDDDEFEDDDDDDDDDCDDDDDDDDDDD
+@HWI-ST628:191:c0299abxx:1:1101:1141:2140 1:N:0:CGATGT
+AGGTTTAAGTGAATATAAGAGCAACAATGACATGAACCAGCCAGGCTTTTGCTTGATGCTGTAATTCAGTGTTTGACCCTGCTGACATTTGTGTTGTCAG
++
+BBCDDFFFHHHHHJIJJJJIJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJJJJJJJJJJJJIJJJJJHHGIJIIHHHHHFFFFFEEEEEEECCDDDDC
+@HWI-ST628:191:c0299abxx:1:1101:1225:2144 1:N:0:CGATGT
+TACAATTATATTAGTATAAAAATGAGCAATTTTTAAAATGAGGCGTGGCATTAAACGTGGCTAATTCATACAAATTCCATATGATAATACTGGTATAAAA
++
+CCCFFFFFHHHHHJHIIJJJJJJJJJJJIJJJJJJIJJJJJJJJJIJJJJJJJJJJJHJJJJJJHHHHHHHFFFFFFEEEEEEDEDDDEDDED@CDEEEC
+@HWI-ST628:191:c0299abxx:1:1101:1036:2155 1:N:0:CGATGT
+TGTTCAGGCTTTTGTTTTAATCAGAGCCTTTTATTTTTAGGACTAATAACTCTGTCACCCCATTGTTTGGGTTTTTGATGGATGAATATTTTTATTTGGC
++
+@C@FDFFFHHFBHEHHIIIIIIDH>GGEHIGIIIIIIGBBG>BG@GIIIIIIIIGIHDGIGIHIIHHIIBE?EHHBBBCCDCDEBADDEDCDC<CCDC@>

data/test/test_mutations_caller_pipeline.rb

@@ -0,0 +1,55 @@
+require 'test/unit'
+require 'nugen_barcode_splitter'
+
+class NugenBarcodeSplitterTest < Test::Unit::TestCase
+  def setup
+
+  end
+
+  def test_nugen_template
+    template = NugenTemplate.new("fastq-multx", "")
+    assert template.to_s.include?("fastq-multx")
+    assert template.to_s.include?("<%= @fwd %>")
+    temp = template.fill("Lane_3", "33", "~/Lane3/", "bc", "fwd", "rev")
+    assert_equal(temp.to_s, "\n    #!/bin/bash\n    \#$ -pe DJ 4\n    \#$ -l h_vmem=6G\n    \#$ -j y\n    \#$ -N fq.Lane_3.33\n    \#$ -o ~/Lane3//nugen_demultiplexing.log\n\n    fastq-multx  -B bc \\\n      fwd rev \\\n      -o R1_33.%.fq R2_33.%.fq\n")
+  end
+
+  def test_fastq
+    fastq_file = "test/fixtures/invalid.fq"
+    assert_raise RuntimeError do
+      Fastq.new(fastq_file)
+    end
+    fastq_file = "test/fixtures/test.fq"
+    assert_nothing_raised do
+      fastq = Fastq.new(fastq_file)
+    end
+    fastq = Fastq.new(fastq_file)
+    out_file = "test/fixtures/added.fq"
+    fastq.add(4, out_file )
+    assert(!File.zero?(out_file), "#{out_file} is empty!")
+    test = File.open(out_file,'r')
+    line = test.readlines[1]
+    test.pos = 0
+    assert(line.start_with?("NNNN"), "Reads do not start with NNNN")
+    line = test.readlines[3]
+    assert(line.start_with?("@@@@"), "Reads do not start with @@@@")
+    File.delete(out_file)
+  end
+
+  def test_sample_sheet
+    samplesheet = SampleSheet.new("test/fixtures/sample_sheet.csv")
+    assert_equal(samplesheet.barcodes[3], "TTAG")
+    assert_equal(samplesheet.sample_id[4], "RX3")
+
+    samplesheet.create_barcode_txt("test/fixtures/barcode")
+
+  end
+
+  def test_statistics
+    log_file = "test/fixtures/Lane4.log"
+    stats = Statistics.new(log_file, ["R1", "R2", "R12", "R22"])
+    assert_equal(stats.total, 31920000)
+    assert_equal(stats.num_reads[0], 8533927)
+    assert_equal(stats.num_unmatched, 2614681)
+  end
+end

metadata

@@ -0,0 +1,75 @@
+--- !ruby/object:Gem::Specification
+name: nugen_barcode_splitter
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Katharina Hayer
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-02-15 00:00:00.000000000Z
+dependencies: []
+description: ! "This gem is designed to demultiplex reads\n                     produced
+  by Illumina with Nugen\n                     (http://www.nugeninc.com/nugen/) barcodes."
+email:
+- katharinaehayer@gmail.com
+executables:
+- base_adder
+- nugen_barcode_splitter
+extensions: []
+extra_rdoc_files: []
+files:
+- bin/base_adder
+- bin/nugen_barcode_splitter
+- lib/nugen_barcode_splitter.rb
+- lib/nugen_barcode_splitter/fastq.rb
+- lib/nugen_barcode_splitter/nugen_template.rb
+- lib/nugen_barcode_splitter/sample_sheet.rb
+- lib/nugen_barcode_splitter/statistics.rb
+- test/fixtures/Lane4.log
+- test/fixtures/barcode_4.txt
+- test/fixtures/barcode_5.txt
+- test/fixtures/barcode_6.txt
+- test/fixtures/barcode_7.txt
+- test/fixtures/barcode_8.txt
+- test/fixtures/invalid.fq
+- test/fixtures/sample_sheet.csv
+- test/fixtures/test.fq
+- test/test_mutations_caller_pipeline.rb
+homepage: https://github.com/khayer/nugen_barcode_splitter
+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: nugen_barcode_splitter
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Nugen Barcode Splitter for Illumina
+test_files:
+- test/fixtures/Lane4.log
+- test/fixtures/barcode_4.txt
+- test/fixtures/barcode_5.txt
+- test/fixtures/barcode_6.txt
+- test/fixtures/barcode_7.txt
+- test/fixtures/barcode_8.txt
+- test/fixtures/invalid.fq
+- test/fixtures/sample_sheet.csv
+- test/fixtures/test.fq
+- test/test_mutations_caller_pipeline.rb