nugen_barcode_splitter 0.0.11 → 0.0.12

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 . 11
+      V E R S I O N - 0 . 0 . 12 - BETA
       #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
 _____________________________________________________________________________
 
@@ -114,6 +114,8 @@ sample_sheet.create_barcode_txt("#{options[:out_dir]}/barcode")
 multx_opts = "#{options[:keep_barcode]} #{options[:eol_only]} #{options[:bol_only]} #{options[:mismatches]}"
 nugen_temp = NugenTemplate.new(options[:fastq_multx],multx_opts)
 
+statistics = Statistics.new()
+
 Dir.glob(options[:project_dir]+"/*").each do |p|
   next unless File.directory? p
   next unless p =~ /Sample_Lane/
@@ -151,30 +153,39 @@ Dir.glob(options[:project_dir]+"/*").each do |p|
     end
     # Merging
     merger = Merger.new(fwd,rev,outdir,number,barcodes)
-    merger.merge()
+    stats = merger.merge()
+    stats_file = File.open("#{outdir}/nugen_demultiplexing.log", 'a')
+    stats_file.puts(stats)
+    stats_file.close()
   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
+  Dir.glob(outdir+"/*").each do |f|
+    if f =~ /nugen_demultiplexing.log/
+      sample_sheet.lanes
+      statistics = Statistics.new(f)
+      stats_out = outdir + "/statistics"
+      stats_handler = File.new(stats_out,'w')
+      stats_handler.write(statistics.to_s)
+      stats_handler.close()
+    end
+    next unless f =~ /_updated/
+    name = f.split("/")[-1]
+    id = name.split(".")[1]
+    sample_dir = outdir + "/Sample_#{id}"
+    begin
+      FileUtils.mkdir_p sample_dir unless File.directory? sample_dir
+    rescue Exception => e
+      STDERR.puts e.message
+    end
+    name = name.gsub(/_updated/, "")
+    cmd = `mv #{f} #{sample_dir}/name`
+    if options[:debug]
+      STDERR.puts cmd if options[:debug]
+    else
+      status = system(cmd)
+      raise "Was not able to rename and move file #{f}!" if status!=true
+    end
+  end
 
 end

data/lib/nugen_barcode_splitter/merger.rb

@@ -49,22 +49,26 @@ class Merger
   #end
 
   def merge()
+    statistics = Array.new(@sample_ids.length()+2,0)
+
     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')
+    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')
+      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|
+      statistics[-1] += 1
       rev_line = rev_file.readline()
       rev_name = rev_line.split(" ")
       fwd_name = fwd_line.split(" ")
@@ -72,9 +76,11 @@ class Merger
 
       @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
+          compare_line_fwd = fwd_splitted_files[i].readline()
+          name_compare_fwd = compare_line_fwd.split(" ")
+          if fwd_line[0] == name_compare_fwd[0] && marker
             marker = false
+            statistics[i] += 1
             fwd_out_files[i].write(fwd_line)
             rev_out_files[i].write(rev_line)
             for k in 1..3
@@ -87,21 +93,31 @@ class Merger
             end
             fwd_file.lineno = fwd_file.lineno - 1
             rev_file.lineno = rev_file.lineno - 1
+          else
+            #puts compare_line_fwd
+            fwd_splitted_files[i].pos = fwd_splitted_files[i].pos - compare_line_fwd.length()
           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]
+          compare_line_rev = rev_splitted_files[i].readline()
+          name_compare_rev = compare_line_rev.split(" ")
+          if name_compare_rev[0] == name_compare_fwd[0]
             for k in 1..3
-              rev_splitted_files[i].readline()
+              compare_line_rev = rev_splitted_files[i].readline()
             end
+          else
+            #puts compare_line_rev
+            rev_splitted_files[i].pos = rev_splitted_files[i].pos - compare_line_rev.length()
           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
+          compare_line_rev = rev_splitted_files[i].readline()
+          name_compare_rev = compare_line_rev.split(" ")
+          if rev_name[0] == name_compare_rev[0] && marker
             marker = false
+            statistics[i] += 1
             fwd_out_files[i].write(fwd_line)
             rev_out_files[i].write(rev_line)
             for k in 1..3
@@ -114,12 +130,15 @@ class Merger
             end
             fwd_file.lineno = fwd_file.lineno - 1
             rev_file.lineno = rev_file.lineno - 1
+          else
+            rev_splitted_files[i].pos = rev_splitted_files[i].pos - compare_line_rev.length()
           end
         end
         break if !marker
       end
 
       if marker
+        statistics[-2] += 1
         fwd_out_unmatched.write(fwd_line)
         rev_out_unmatched.write(rev_line)
         for k in 1..3
@@ -127,9 +146,12 @@ class Merger
           fwd_out_unmatched.write(fwd_file.readline())
         end
       end
-
     end
-
-
+    stats = ""
+    @sample_ids.each_with_index do |id,i|
+      stats += id +"/t" + statistics[i].to_s + "/n"
+    end
+    stats += "unmatched/t" + statistics[-2].to_s + "/n"
+    stats += "total/t" + statistics[-1].to_s + "/n"
   end
 end

data/lib/nugen_barcode_splitter/nugen_template.rb

@@ -3,27 +3,25 @@ require "erubis"
 class NugenTemplate
 
   def initialize(fastq_multx, options)
-    @template =<<EOF
-gunzip -c <%= @read %> | #{fastq_multx} \\
-  --bcfile <%= @barcodes %> #{options} <%= @options %> \\
-  --prefix <%= @lane_dir %>/<%= @direction %> \\
-  --suffix ".fq"
-EOF
 #    @template =<<EOF
-##{fastq_multx} #{options}  <%= @barcodes %> \\
-#  <(gunzip -c <%= @read %>) \\
-#  -o <%= @lane_dir %>/<%= @direction %>.%.fq  \\
-#  >> <%= @lane_dir %>/nugen_demultiplexing.log
+#gunzip -c <%= @read %> | #{fastq_multx} \\
+#  --bcfile <%= @barcodes %> #{options} <%= @options %> \\
+#  --prefix <%= @lane_dir %>/<%= @direction %> \\
+#  --suffix ".fq"
 #EOF
+    @template =<<EOF
+#{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, read, is_fwd)
     if is_fwd
       direction = "R1_#{number}_"
-      options = "--bol"
     else
       direction = "R2_#{number}_"
-      options = "--eol"
     end
     context = {
       :lane => lane,
@@ -32,7 +30,7 @@ EOF
       :barcodes => barcodes,
       :read => read,
       :direction => direction,
-      :options => options
+      #:options => options
     }
 
     eruby = Erubis::Eruby.new(@template)

data/lib/nugen_barcode_splitter/statistics.rb

@@ -1,3 +1,4 @@
+require 'csv'
 class Statistics
 
   def initialize(lane_log)

data/test/test_mutations_caller_pipeline.rb

@@ -54,11 +54,12 @@ class NugenBarcodeSplitterTest < Test::Unit::TestCase
   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",
+    merger = Merger.new("test/fixtures/Sample_Lane5/k.gz",
+      "test/fixtures/Sample_Lane5/l.gz",
       "test/fixtures/Sample_Lane5", "001", "test/fixtures/barcode_5.txt")
     assert_equal(merger.sample_ids, ["RX3", "RX4", "RX3X2", "RX4X2"])
-    #merger.merge
+    stats = merger.merge()
+    assert_equal([28, 18, 26, 21, 7],stats)
     #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: 0.0.11
+  version: 0.0.12
   prerelease: 
 platform: ruby
 authors: