nugen_barcode_splitter 0.0.16 → 0.0.17

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 . 16 - BETA
+      V E R S I O N - 0 . 0 . 17 - BETA
       #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
 _____________________________________________________________________________
 
@@ -34,7 +34,8 @@ options = {
   :mismatches => "",
   :keep_barcode => "",
   :fastq_multx => "fastq_multx",
-  :debug => false
+  :debug => false,
+  :lane_number => ""
 }
 
 optparse = OptionParser.new do |opts|
@@ -74,6 +75,10 @@ optparse = OptionParser.new do |opts|
     options[:mismatches] = "-m #{i}" if i
   end
 
+  opts.on("-n","--laneNumber NUM", String, "Specific lane number (Default:all lanes)") do |i|
+    options[:lane_number] = i if i
+  end
+
   opts.on("-x", "--fastq_multx DIR", String) do |i|
     options[:fastq_multx] = i if i
   end
@@ -114,10 +119,9 @@ 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)
 
-
 Dir.glob(options[:project_dir]+"/*").each do |p|
   next unless File.directory? p
-  next unless p =~ /Sample_Lane/
+  next unless p =~ /Sample_Lane#{options[:lane_number]}/
   outdir = ""
   lane = ""
   Dir.glob(p+"/*").each do |fwd|

data/lib/nugen_barcode_splitter/merger.rb

@@ -78,7 +78,7 @@ class Merger
         if !fwd_splitted_files[i].eof?
           compare_line_fwd = fwd_splitted_files[i].readline()
           name_compare_fwd = compare_line_fwd.split(" ")
-          if fwd_line[0] == name_compare_fwd[0] && marker
+          if fwd_name[0] == name_compare_fwd[0] && marker
             marker = false
             statistics[i] += 1
             fwd_out_files[i].write(fwd_line)
@@ -86,9 +86,9 @@ class Merger
             for k in 1..3
               fwd_file.readline()
               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.gsub(/^[A-Z]{4}/,"NNNN")) 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
+              fwd_out_files[i].write(compare_line_fwd.gsub(/^[\S]{4}/,"@@@@")) if k == 3
               rev_out_files[i].write(rev_file.readline())
             end
             fwd_file.lineno = fwd_file.lineno - 1
@@ -123,9 +123,9 @@ class Merger
             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.gsub(/[A-Z]{4}$/,"NNNN")) if k == 1
               rev_out_files[i].write(compare_line_rev) if k == 2
-              rev_out_files[i].write("@@@@"+compare_line_rev) if k == 3
+              rev_out_files[i].write(compare_line_rev.gsub(/[\S]{4}$/,"@@@@")) if k == 3
               fwd_out_files[i].write(fwd_file.readline())
             end
             fwd_file.lineno = fwd_file.lineno - 1

data/lib/nugen_barcode_splitter/nugen_template.rb

@@ -3,25 +3,27 @@ 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_fastq_multx.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_fastq_multx.log
+#EOF
   end
 
   def fill(lane, number, lane_dir, barcodes, read, is_fwd)
     if is_fwd
-      direction = "R1_#{number}"
+      direction = "R1_#{number}."
+      options = "--bol"
     else
-      direction = "R2_#{number}"
+      direction = "R2_#{number}."
+      options = "--eol"
     end
     context = {
       :lane => lane,
@@ -30,7 +32,7 @@ EOF
       :barcodes => barcodes,
       :read => read,
       :direction => direction,
-      #:options => options
+      :options => options
     }
 
     eruby = Erubis::Eruby.new(@template)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nugen_barcode_splitter
 version: !ruby/object:Gem::Version
-  version: 0.0.16
+  version: 0.0.17
   prerelease: 
 platform: ruby
 authors: