nugen_barcode_splitter 0.0.9 → 0.0.10

data/bin/nugen_barcode_splitter

@@ -5,7 +5,7 @@ require "nugen_barcode_splitter"
 require "fileutils"
 
 usage =<<EOF
-      V E R S I O N - 0 . 0 . 8
+      V E R S I O N - 0 . 0 . 10
       #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
 _____________________________________________________________________________
 
@@ -134,32 +134,47 @@ Dir.glob(options[:project_dir]+"/*").each do |p|
     rescue Exception => e
       STDERR.puts e.message
     end
-    cmd = nugen_temp.fill(lane,number,outdir, barcodes, fwd, rev)
+    # Fwd_read
+    cmd = nugen_temp.fill(lane,number,outdir, barcodes, fwd, true)
     if options[:debug]
       STDERR.puts cmd if options[:debug]
     else
       status = system('bash', '-c', cmd)
-      raise "Calling the template did not succeed!" if !status
+      raise "Calling the template for fwd did not succeed!" if !status
     end
-  end
-
-  # Add the trimmed bases
-  Dir.glob(outdir+"/*").each do |fwd|
-    if fwd =~ /nugen_demultiplexing.log/
-      sample_sheet.lanes
-      statistics = Statistics.new(fwd)
-    end
-    next unless fwd =~ /R1_[0-9]{3}./
-    cmd = "base_adder #{fwd} 4 #{fwd}_added"
+    cmd = nugen_temp.fill(lane,number,outdir, barcodes, rev, false)
     if options[:debug]
       STDERR.puts cmd if options[:debug]
     else
-      status = system(cmd)
-      raise "Calling base_adder did not succeed!" if !status
-      cmd = "mv #{fwd}_added #{fwd}"
-      status = system(cmd)
-      raise "Was not able to rename file #{fwd}!" if status!=true
+      status = system('bash', '-c', cmd)
+      raise "Calling the template for rev did not succeed!" if !status
     end
+    # Merging
+    merger = Merger.new(fwd,rev,outdir,number,barcodes)
+    merger.merge()
   end
 
+  # Add the trimmed bases
+  #Dir.glob(outdir+"/*").each do |fwd|
+  #  if fwd =~ /nugen_demultiplexing.log/
+  #    sample_sheet.lanes
+  #    statistics = Statistics.new(fwd)
+  #    stats_out = outdir + "/statistics"
+  #    stats_handler = File.new(stats_out,'w')
+  #    stats_handler.write(statistics.to_s)
+  #    stats_handler.close()
+  #  end
+  #  next unless fwd =~ /R1_[0-9]{3}./
+  #  cmd = "base_adder #{fwd} 4 #{fwd}_added"
+  #  if options[:debug]
+  #    STDERR.puts cmd if options[:debug]
+  #  else
+  #    status = system(cmd)
+  #    raise "Calling base_adder did not succeed!" if !status
+  #    cmd = "mv #{fwd}_added #{fwd}"
+  #    status = system(cmd)
+  #    raise "Was not able to rename file #{fwd}!" if status!=true
+  #  end
+  #end
+
 end

data/lib/nugen_barcode_splitter/merger.rb

@@ -0,0 +1,132 @@
+require "zlib"
+
+class Merger
+  def initialize(fwd,rev,outdir,number,barcodes)
+    # get sampleID
+    @values_fwd = []
+    @values_rev = []
+    @sample_ids = []
+    i = 0
+    File.open(barcodes).each do |line|
+      next if line.include?("#")
+      line = line.split(" ")
+      @sample_ids[i] = line[0]
+      i += 1
+    end
+    @fwd = fwd
+    @rev = rev
+    @outdir = outdir
+    @number = number
+  end
+
+  attr_accessor :sample_ids, :values_fwd, :values_rev
+
+  #def prepare_hash()
+  #  @sample_ids.each_with_index do |sample_id, i|
+  #    a = Thread.new {
+  #      filehandler = File.open(@outdir+"/R1_#{@number}.#{sample_id}.fq")
+  #      filehandler.each do |line|
+  #        next unless line.include?("@HWI-")
+  #        line = line.split(" ")
+  #        name = line[0].split(":")[4..-1].join(":")
+  #        @values_fwd[i].store(name,filehandler.pos)
+  #      end
+  #      filehandler.close()
+  #    }
+  #    b = Thread.new {
+  #      filehandler = File.open(@outdir+"/R2_#{@number}.#{sample_id}.fq")
+  #      filehandler.each do |line|
+  #        next unless line.include?("@HWI-")
+  #        line = line.split(" ")
+  #        name = line[0].split(":")[4..-1].join(":")
+  #        @values_rev[i].store(name,filehandler.pos)
+  #      end
+  #      filehandler.close()
+  #    }
+  #    a.join
+  #    b.join
+  #  end
+  #end
+
+  def merge()
+    fwd_file = Zlib::GzipReader.open(@fwd)
+    rev_file = Zlib::GzipReader.open(@rev)
+    fwd_splitted_files = []
+    rev_splitted_files = []
+    fwd_out_files = []
+    rev_out_files = []
+    fwd_out_unmatched = File.open(@outdir+"/R1_#{@number}.unmatched_updated.fq",'w')
+    rev_out_unmatched = File.open(@outdir+"/R2_#{@number}.unmatched_updated.fq",'w')
+    @sample_ids.each_with_index do |sample_id, i|
+      fwd_splitted_files[i] = File.open(@outdir+"/R1_#{@number}.#{sample_id}.fq")
+      rev_splitted_files[i] = File.open(@outdir+"/R2_#{@number}.#{sample_id}.fq")
+      #OUTFILES????
+      fwd_out_files[i] = File.open(@outdir+"/R1_#{@number}.#{sample_id}_updated.fq",'w')
+      rev_out_files[i] = File.open(@outdir+"/R2_#{@number}.#{sample_id}_updated.fq",'w')
+    end
+    fwd_file.each do |fwd_line|
+      rev_line = rev_file.readline()
+      rev_name = rev_line.split(" ")
+      fwd_name = fwd_line.split(" ")
+      marker = true
+
+      @sample_ids.each_with_index do |sample_id, i|
+        if !fwd_splitted_files[i].eof?
+          compare_line_fwd = fwd_splitted_files[i].readline().split(" ")
+          if fwd_line[0] == compare_line_fwd[0] && marker
+            marker = false
+            fwd_out_files[i].write(fwd_line)
+            rev_out_files[i].write(rev_line)
+            for k in 1..3
+              fwd_file.readline()
+              rev_splitted_files[i].readline if marker2
+              compare_line_fwd = fwd_splitted_files[i].readline()
+              fwd_out_files[i].write("NNNN"+compare_line_fwd) if k == 1
+              fwd_out_files[i].write(compare_line_fwd) if k == 2
+              fwd_out_files[i].write("@@@@"+compare_line_fwd) if k == 3
+              rev_out_files[i].write(rev_file.readline())
+            end
+          end
+        end
+        if !marker && !rev_splitted_files[i].eof?
+          compare_line_rev = rev_splitted_files[i].readline().split(" ")
+          if compare_line_rev[0] == compare_line_fwd[0]
+            for k in 1..3
+              rev_splitted_files[i].readline()
+            end
+          end
+        end
+        break if !marker
+        if !rev_splitted_files[i].eof?
+          compare_line_rev = rev_splitted_files[i].readline().split(" ")
+          if rev_name[0] == compare_line_rev[0] && marker
+            marker = false
+            fwd_out_files[i].write(fwd_line)
+            rev_out_files[i].write(rev_line)
+            for k in 1..3
+              rev_file.readline()
+              compare_line_rev = rev_splitted_files[i].readline()
+              rev_out_files[i].write("NNNN"+compare_line_rev) if k == 1
+              rev_out_files[i].write(compare_line_rev) if k == 2
+              rev_out_files[i].write("@@@@"+compare_line_rev) if k == 3
+              fwd_out_files[i].write(fwd_file.readline())
+            end
+          end
+        end
+        break if !marker
+      end
+
+      if marker
+        fwd_out_unmatched.write(fwd_line)
+        rev_out_unmatched.write(rev_line)
+        for k in 1..3
+          rev_out_unmatched.write(rev_file.readline())
+          fwd_out_unmatched.write(fwd_file.readline())
+        end
+      end
+
+    end
+
+
+  end
+end

data/lib/nugen_barcode_splitter/nugen_template.rb

@@ -4,25 +4,26 @@ class NugenTemplate
 
   def initialize(fastq_multx, options)
     @template =<<EOF
-#{fastq_multx} #{options} <%= @barcodes %> \\
-  <(gunzip -c <%= @fwd %>) \\
-  <(gunzip -c <%= @rev %>) \\
-  -o <%= @lane_dir %>/<%= @r1 %>.%.fq <%= @lane_dir %>/<%= @r2 %>.%.fq \\
+#{fastq_multx} #{options}  <%= @barcodes %> \\
+  <(gunzip -c <%= @read %>) \\
+  -o <%= @lane_dir %>/<%= @direction %>.%.fq  \\
   >> <%= @lane_dir %>/nugen_demultiplexing.log
 EOF
   end
 
-  def fill(lane, number, lane_dir, barcodes, fwd, rev)
-
+  def fill(lane, number, lane_dir, barcodes, read, is_fwd)
+    if is_fwd
+      direction = "R1_#{number}"
+    else
+      direction = "R2_#{number}"
+    end
     context = {
       :lane => lane,
       :number => number,
       :lane_dir => lane_dir,
       :barcodes => barcodes,
-      :fwd => fwd,
-      :rev => rev,
-      :r1 => "R1_#{number}",
-      :r2 => "R2_#{number}"
+      :read => read,
+      :direction => direction
     }
 
     eruby = Erubis::Eruby.new(@template)

data/lib/nugen_barcode_splitter.rb

@@ -2,7 +2,7 @@ require "nugen_barcode_splitter/nugen_template"
 require "nugen_barcode_splitter/fastq"
 require "nugen_barcode_splitter/sample_sheet"
 require "nugen_barcode_splitter/statistics"
-
+require "nugen_barcode_splitter/merger.rb"
 class NugenBarcodeSplitter
 
 end

data/test/test_mutations_caller_pipeline.rb

@@ -9,9 +9,9 @@ class NugenBarcodeSplitterTest < Test::Unit::TestCase
   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, "fastq-multx  bc \\\n  <(gunzip -c fwd) \\\n  <(gunzip -c rev) \\\n  -o ~/Lane3//R1_33.%.fq ~/Lane3//R2_33.%.fq \\\n  >> ~/Lane3//nugen_demultiplexing.log\n")
+    assert template.to_s.include?("<%= @read %>")
+    temp = template.fill("Lane_3", "33", "~/Lane3/", "bc", "fwd", true)
+    assert_equal(temp.to_s, "fastq-multx   bc \\\n  <(gunzip -c fwd) \\\n  -o ~/Lane3//R1_33.%.fq  \\\n  >> ~/Lane3//nugen_demultiplexing.log\n")
   end
 
   def test_fastq
@@ -52,4 +52,13 @@ class NugenBarcodeSplitterTest < Test::Unit::TestCase
     assert_equal(stats.num_reads[0], 8533927)
     assert_equal(stats.num_unmatched, 2614681)
   end
+
+  def test_merger
+    merger = Merger.new("test/fixtures/Sample_Lane5/Lane5_NoIndex_L005_R1_001.fastq.gz",
+      "test/fixtures/Sample_Lane5/Lane5_NoIndex_L005_R2_001.fastq.gz",
+      "test/fixtures/Sample_Lane5", "001", "test/fixtures/barcode_5.txt")
+    assert_equal(merger.sample_ids, ["RX3", "RX4", "RX3X2", "RX4X2"])
+    #merger.merge
+    #assert.equal(merger.values_fwd[1].value_at(),{"sfggf"=>"dffg"})
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nugen_barcode_splitter
 version: !ruby/object:Gem::Version
-  version: 0.0.9
+  version: 0.0.10
   prerelease: 
 platform: ruby
 authors:
@@ -25,6 +25,7 @@ files:
 - bin/nugen_barcode_splitter
 - lib/nugen_barcode_splitter.rb
 - lib/nugen_barcode_splitter/fastq.rb
+- lib/nugen_barcode_splitter/merger.rb
 - lib/nugen_barcode_splitter/nugen_template.rb
 - lib/nugen_barcode_splitter/sample_sheet.rb
 - lib/nugen_barcode_splitter/statistics.rb