nugen_barcode_splitter 0.0.1 → 0.0.2

data/bin/nugen_barcode_splitter

@@ -1,7 +1,8 @@
 #!/usr/bin/env ruby
-require "rubygems"
 require "yaml"
 require "optparse"
+require "nugen_barcode_splitter"
+require "fileutils"
 
 usage =<<EOF
       #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
@@ -112,21 +113,21 @@ 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|
+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
+  lane = ""
+  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/,"")
+    lane = tmp[0].gsub(/\D/,"")
+    number = tmp[4].gsub(/\D/,"")
     barcodes = "#{options[:out_dir]}/barcode_#{lane}.txt"
-    outdir = options[:outdir] + "/Lane#{lane}"
+    outdir = options[:out_dir] + "Lane#{lane}"
     begin
       FileUtils.mkdir_p outdir unless File.directory? outdir
     rescue Exception => e
@@ -134,7 +135,7 @@ Dir.glob(options[:project_dir]).each do |p|
     end
     cmd = nugen_temp.fill(lane,number,outdir, barcodes, fwd, rev)
     if options[:debug]
-      puts cmd if options[:debug]
+      STDERR.puts cmd if options[:debug]
     else
       status = system(cmd)
       raise "Calling the template did not succeed!" if !status
@@ -142,14 +143,21 @@ Dir.glob(options[:project_dir]).each do |p|
   end
 
   # Add the trimmed bases
-  Dir.glob(outdir).each do |fwd|
+  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 = "base_adder #{fwd} 4 #{fwd}_added"
     if options[:debug]
-      puts cmd if options[:debug]
+      STDERR.puts cmd if options[:debug]
     else
       status = system(cmd)
       raise "Calling the template did not succeed!" if !status
+      cmd = "mv #{fwd}_added #{fwd}"
+      status = system(cmd)
+      raise "Was not ablde to rename file #{fwd}!" if status!=true
     end
   end
 

data/lib/nugen_barcode_splitter/nugen_template.rb

@@ -14,7 +14,8 @@ class NugenTemplate
 
     #{fastq_multx} #{options} -B <%= @barcodes %> \\
       <(gunzip -c <%= @fwd %>) <(gunzip -c <%= @rev %>) \\
-      -o <%= @lane_dir %>/<%= @r1 %>.%.fq <%= @lane_dir %>/<%= @r2 %>.%.fq
+      -o <%= @lane_dir %>/<%= @r1 %>.%.fq <%= @lane_dir %>/<%= @r2 %>.%.fq \\
+      >> <%= @lane_dir %>/nugen_demultiplexing.log
 EOF
   end
 

data/lib/nugen_barcode_splitter/sample_sheet.rb

@@ -21,7 +21,7 @@ class SampleSheet
     end
   end
 
-  attr_accessor :lanes, :sample_id, :barcodes
+  attr_accessor :lanes, :sample_id, :barcodes, :barcode_lengths
 
   def create_barcode_txt(prefix)
     current_lane = "dummy"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nugen_barcode_splitter
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors: