fastq-factory 0.1.4 → 0.1.5

data/VERSION

@@ -1 +1 @@
-0.1.4
+0.1.5

data/bin/fastq-factory

@@ -26,8 +26,8 @@ reverse_reads_suffix, reverse_reads_file_extension = options[:reverse_reads_suff
 sample_map = extract_file_prefixes_and_sample_name(options[:sample_map_file], options[:directory])
 # check sequence files exist
 sample_map.keys.each do |sample_prefix|
-  file_exists?("#{sample_prefix}#{options[:forward_reads_suffix]}", options[:directory])
-  file_exists?("#{sample_prefix}#{options[:reverse_reads_suffix]}", options[:directory])
+  file_exists?(options[:directory], "#{sample_prefix}#{options[:forward_reads_suffix]}")
+  file_exists?(options[:directory], "#{sample_prefix}#{options[:reverse_reads_suffix]}")
 end
 if options[:trim]
   fastq_quality_trimmer_path = find_executable("fastq_quality_trimmer", options[:fastq_quality_trimmer_dir])
@@ -40,8 +40,8 @@ end
 
 if options[:metrics]
   sample_map.keys.each do |sample_prefix|
-    file_exists?("#{sample_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}", options[:directory])
-    file_exists?("#{sample_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}", options[:directory])
+    file_exists?(options[:directory], "#{sample_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}", "#{sample_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+    file_exists?(options[:directory], "#{sample_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}", "#{sample_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
   end
   generate_quality_metrics(sample_map, options[:directory], options[:forward_reads_suffix], options[:reverse_reads_suffix], options[:quality_scale], options[:metrics_quality_cutoff])
 end

data/fastq-factory.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "fastq-factory"
-  s.version = "0.1.4"
+  s.version = "0.1.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Anthony Underwood"]
-  s.date = "2012-08-24"
+  s.date = "2012-08-29"
   s.description = "This tool can process fastq files, using fastq_quality_trimmer and quake to correct fastq files and then provide a quality asssessment of the data"
   s.email = "anthony.underwood@hpa.org.uk"
   s.executables = ["fastq-factory"]

data/lib/fastq-factory.rb

@@ -10,8 +10,12 @@ def extract_file_prefixes_and_sample_name(sample_map_file, directory)
   return sample_map
 end
 
-def file_exists?(filename, directory)
-  abort("You specified a fastq file : #{filename}. This does not exist! Please check your sample map file") unless File.exists?("#{directory}/#{filename}")
+def file_exists?(directory, *filenames)
+  at_least_one_file_found = false
+  filenames.each do |filename|
+    at_least_one_file_found = true  if File.exists?("#{directory}/#{filename}")
+  end
+  abort("You specified a file(s): #{filenames.join(", ")}. At least one of these must exist! Please check your sample map file") unless at_least_one_file_found
 end
 
 def find_executable(executable_name, directory = nil)

data/lib/generate_quality_metrics.rb

@@ -6,41 +6,57 @@ include MiseqRunStats
 def generate_quality_metrics(sample_map, directory, forward_reads_suffix, reverse_reads_suffix, quality_scale, quality_cutoff)
   if File.exists?("#{directory}/ResequencingRunStatistics.xml")
     puts "Assessing quality from Miseq run stats file"
-    resequencing_run_stats = parse_resequencing_run_stats("#{directory}/ResequencingRunStatistics.xml", sample_map.values)
+    run_stats = parse_run_stats("#{directory}/ResequencingRunStatistics.xml", sample_map.values)
+  elsif File.exists?("#{directory}/AssemblyRunStatistics.xml")
+    puts "Assessing quality from Miseq run stats file"
+    run_stats = parse_assembly_run_stats("#{directory}/AssemblyRunStatistics.xml", sample_map.values)
   else
-    resequencing_run_stats = ResequencingRunStats.new
-    resequencing_run_stats.sample_stats = Hash.new
+    run_stats = ResequencingRunStats.new
+    run_stats.sample_stats = Hash.new
     sample_map.values.each do |sample_name|
-      resequencing_run_stats.sample_stats[sample_name] = SampleStats.new
+      run_stats.sample_stats[sample_name] = ResequencingSampleStats.new
     end
   end
 
+  forward_reads_trimmed_suffix = forward_reads_suffix.sub(/(.+)(\..+?)$/, '\1.trimmed\2')
+  reverse_reads_trimmed_suffix = reverse_reads_suffix.sub(/(.+)(\..+?)$/, '\1.trimmed\2')
 
   forward_reads_trimmed_corrected_suffix = forward_reads_suffix.sub(/(.+)(\..+?)$/, '\1.trimmed.cor\2')
   reverse_reads_trimmed_corrected_suffix = reverse_reads_suffix.sub(/(.+)(\..+?)$/, '\1.trimmed.cor\2')
 
-
   sample_map.each do |read_file_prefix, sample_name|
     puts "Assesing quality for #{sample_name}"
-    resequencing_run_stats.sample_stats[sample_name].fastq_stats = Hash.new
-    resequencing_run_stats.sample_stats[sample_name].fastq_stats["forward"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{forward_reads_suffix}",quality_scale, quality_cutoff)
-    resequencing_run_stats.sample_stats[sample_name].fastq_stats["reverse"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{reverse_reads_suffix}",quality_scale, quality_cutoff)
-    resequencing_run_stats.sample_stats[sample_name].fastq_stats["forward-trim_corrected"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{forward_reads_trimmed_corrected_suffix}",quality_scale, quality_cutoff)
-    resequencing_run_stats.sample_stats[sample_name].fastq_stats["forward-trim_corrected"].percentage_compared_to_raw = percentage_compared_to_raw("#{directory}/#{read_file_prefix}#{forward_reads_trimmed_corrected_suffix}", "#{directory}/#{read_file_prefix}#{forward_reads_suffix}")
-    resequencing_run_stats.sample_stats[sample_name].fastq_stats["reverse-trim_corrected"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{reverse_reads_trimmed_corrected_suffix}",quality_scale, quality_cutoff)
-    resequencing_run_stats.sample_stats[sample_name].fastq_stats["reverse-trim_corrected"].percentage_compared_to_raw = percentage_compared_to_raw("#{directory}/#{read_file_prefix}#{reverse_reads_trimmed_corrected_suffix}", "#{directory}/#{read_file_prefix}#{reverse_reads_suffix}")
+    run_stats.sample_stats[sample_name].fastq_stats = Hash.new
+    run_stats.sample_stats[sample_name].fastq_stats["forward"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{forward_reads_suffix}",quality_scale, quality_cutoff)
+    run_stats.sample_stats[sample_name].fastq_stats["reverse"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{reverse_reads_suffix}",quality_scale, quality_cutoff)
+    if File.exists?("#{directory}/#{read_file_prefix}#{forward_reads_trimmed_corrected_suffix}")
+      run_stats.sample_stats[sample_name].fastq_stats["forward-trim_corrected"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{forward_reads_trimmed_corrected_suffix}",quality_scale, quality_cutoff)
+      run_stats.sample_stats[sample_name].fastq_stats["forward-trim_corrected"].percentage_compared_to_raw = percentage_compared_to_raw("#{directory}/#{read_file_prefix}#{forward_reads_trimmed_corrected_suffix}", "#{directory}/#{read_file_prefix}#{forward_reads_suffix}")
+      run_stats.sample_stats[sample_name].fastq_stats["reverse-trim_corrected"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{reverse_reads_trimmed_corrected_suffix}",quality_scale, quality_cutoff)
+      run_stats.sample_stats[sample_name].fastq_stats["reverse-trim_corrected"].percentage_compared_to_raw = percentage_compared_to_raw("#{directory}/#{read_file_prefix}#{reverse_reads_trimmed_corrected_suffix}", "#{directory}/#{read_file_prefix}#{reverse_reads_suffix}")
+    else
+      run_stats.sample_stats[sample_name].fastq_stats["forward-trim_corrected"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{forward_reads_trimmed_suffix}",quality_scale, quality_cutoff)
+      run_stats.sample_stats[sample_name].fastq_stats["forward-trim_corrected"].percentage_compared_to_raw = percentage_compared_to_raw("#{directory}/#{read_file_prefix}#{forward_reads_trimmed_suffix}", "#{directory}/#{read_file_prefix}#{forward_reads_suffix}")
+      run_stats.sample_stats[sample_name].fastq_stats["reverse-trim_corrected"] = generate_quality_stats_for_read("#{directory}/#{read_file_prefix}#{reverse_reads_trimmed_suffix}",quality_scale, quality_cutoff)
+      run_stats.sample_stats[sample_name].fastq_stats["reverse-trim_corrected"].percentage_compared_to_raw = percentage_compared_to_raw("#{directory}/#{read_file_prefix}#{reverse_reads_trimmed_suffix}", "#{directory}/#{read_file_prefix}#{reverse_reads_suffix}")
+    end
+
   end
   # print out data
   output_file = File.open("#{directory}/summary_stats.txt", "w")
   # print headers
-  output_file.puts "run name\tnumber of bases(Gb)\tnumber of clusters\tsample name\tdirection\tnumber of clusters\tnumber of forward reads aligned\tnumber of reverse reads aligned\tcoverage\tnumber of snps\tmean quality\tread base where qual falls below 30\tpercent reduction compared to raw"
-  output_file.puts "#{directory.match(/.*\/(.+?)$/).captures.first}\t#{resequencing_run_stats.number_of_bases}\t#{resequencing_run_stats.number_of_clusters}"
-  resequencing_run_stats.sample_stats.keys.sort.each do |sample_name|
-    sample_stats = resequencing_run_stats.sample_stats[sample_name]
-    output_file.puts "\t\t\t#{sample_name}\t\t#{sample_stats.number_of_clusters}\t#{sample_stats.number_of_forward_reads_aligned}\t#{sample_stats.number_of_reverse_reads_aligned}\t#{sample_stats.coverage}\t#{sample_stats.number_of_snps}"
+  output_file.puts "run name\tnumber of bases(Gb)\tnumber of clusters\tsample name\tdirection\tnumber of clusters\tnumber of forward reads aligned\tnumber of reverse reads aligned\tcoverage\tnumber of snps\tnumber of contigs\tmean contig size\tn50\tnumber of bases\tmean quality\tread base where qual falls below 30\tpercent reduction compared to raw"
+  output_file.puts "#{directory.match(/.*\/(.+?)$/).captures.first}\t#{run_stats.number_of_bases}\t#{run_stats.number_of_clusters}"
+  run_stats.sample_stats.keys.sort.each do |sample_name|
+    sample_stats = run_stats.sample_stats[sample_name]
+    if sample_stats.class == Struct::ResequencingSampleStats
+      output_file.puts "\t\t\t#{sample_name}\t\t#{sample_stats.number_of_clusters}\t#{sample_stats.number_of_forward_reads_aligned}\t#{sample_stats.number_of_reverse_reads_aligned}\t#{sample_stats.coverage}\t#{sample_stats.number_of_snps}"
+    elsif sample_stats.class == Struct::AssemblySampleStats
+      output_file.puts "\t\t\t#{sample_name}\t\t#{sample_stats.number_of_clusters}\t\t\t\t\t#{sample_stats.number_of_contigs}\t#{sample_stats.mean_contig_size}\t#{sample_stats.n50}\t#{sample_stats.number_of_bases}"
+    end
     ["forward", "reverse", "forward-trim_corrected", "reverse-trim_corrected"].each do |direction|
-      fastq_stats = resequencing_run_stats.sample_stats[sample_name].fastq_stats[direction]
-      output_file.puts "\t\t\t\t#{direction}\t\t\t\t\t\t#{fastq_stats.mean_quality}\t#{fastq_stats.position_where_quality_lt_20}\t#{fastq_stats.percentage_compared_to_raw}"
+      fastq_stats = run_stats.sample_stats[sample_name].fastq_stats[direction]
+      output_file.puts "\t\t\t\t#{direction}\t\t\t\t\t\t\t\t\t\t#{fastq_stats.mean_quality}\t#{fastq_stats.position_where_quality_lt_20}\t#{fastq_stats.percentage_compared_to_raw}"
     end
   end
   output_file.close

data/lib/miseq_run_stats.rb

@@ -1,7 +1,9 @@
 module MiseqRunStats
   require 'nokogiri'
   ResequencingRunStats = Struct.new("ResequencingRunStats", :number_of_bases, :number_of_clusters, :sample_stats)
-  SampleStats = Struct.new("SampleStats", :sample_name, :number_of_clusters, :number_of_forward_reads_aligned, :number_of_reverse_reads_aligned, :coverage, :number_of_snps, :fastq_stats)
+  ResequencingSampleStats = Struct.new("ResequencingSampleStats", :sample_name, :number_of_clusters, :number_of_forward_reads_aligned, :number_of_reverse_reads_aligned, :coverage, :number_of_snps, :fastq_stats)
+  AssemblyRunStats = Struct.new("AssemblyRunStats", :number_of_bases, :number_of_clusters, :sample_stats)
+  AssemblySampleStats = Struct.new("AssemblySampleStats", :sample_name, :number_of_clusters, :number_of_contigs, :mean_contig_size, :n50, :number_of_bases, :fastq_stats)
   def parse_resequencing_run_stats(xml_file, original_sample_names = nil)
     xml = Nokogiri::XML(File.read(xml_file))
     resequencing_run_stats = ResequencingRunStats.new
@@ -16,7 +18,7 @@ module MiseqRunStats
       sample_name = summarised_samples_stats.search('SampleName').text
       sample_name = original_sample_names.select{|original_sample_name| sample_name =~ /#{original_sample_name}/}.first unless original_sample_names.nil? # alter sample name to original sample name if supplies as an array
 
-      resequencing_run_stats.sample_stats[sample_name] = SampleStats.new
+      resequencing_run_stats.sample_stats[sample_name] = ResequencingSampleStats.new
       resequencing_run_stats.sample_stats[sample_name].sample_name = sample_name
       resequencing_run_stats.sample_stats[sample_name].number_of_clusters = summarised_samples_stats.search('NumberOfClustersPF').text
       resequencing_run_stats.sample_stats[sample_name].number_of_forward_reads_aligned = summarised_samples_stats.search('ClustersAlignedR1').text
@@ -26,4 +28,41 @@ module MiseqRunStats
     end
     return resequencing_run_stats
   end
+  def parse_assembly_run_stats(xml_file, original_sample_names = nil)
+    xml = Nokogiri::XML(File.read(xml_file))
+    assembly_run_stats = AssemblyRunStats.new
+
+    xml.search('//RunStats').each do |run_stats|
+      assembly_run_stats.number_of_bases = run_stats.search('YieldInBasesPF').text.to_f/1000000000
+      assembly_run_stats.number_of_clusters = run_stats.search('NumberOfClustersPF').text.to_i
+    end
+
+    # get un-named contig data
+    assembly_stats = Array.new
+    xml.search('//AssemblyStatistics').each do |assembly_sample_stats|
+      number_of_contigs = assembly_sample_stats.search('NumberOfContigs').text.to_i
+      mean_contig_size = assembly_sample_stats.search('MeanContigLength').text.to_f.to_i
+      n50 = assembly_sample_stats.search('N50').text.to_i
+      number_of_bases = assembly_sample_stats.search('BaseCount').text.to_i
+      assembly_stats << {:number_of_contigs  => number_of_contigs, :mean_contig_size => mean_contig_size, :n50 => n50, :number_of_bases => number_of_bases}
+    end
+
+    assembly_run_stats.sample_stats = Hash.new
+    xml.search('//SampleStatistics').each do |sample_stats|
+      sample_name = sample_stats.search('SampleName').text
+      sample_name = original_sample_names.select{|original_sample_name| sample_name =~ /#{original_sample_name}/}.first unless original_sample_names.nil? # alter sample name to original sample name if supplies as an array
+      next if sample_name.nil?
+
+      assembly_run_stats.sample_stats[sample_name] = AssemblySampleStats.new
+      assembly_run_stats.sample_stats[sample_name].sample_name = sample_name
+      assembly_run_stats.sample_stats[sample_name].number_of_clusters = sample_stats.search('NumberOfClustersPF').text
+      assembly_sample_stats = assembly_stats.shift
+      assembly_run_stats.sample_stats[sample_name].number_of_contigs = assembly_sample_stats[:number_of_contigs]
+      assembly_run_stats.sample_stats[sample_name].mean_contig_size = assembly_sample_stats[:mean_contig_size]
+      assembly_run_stats.sample_stats[sample_name].n50 = assembly_sample_stats[:n50]
+      assembly_run_stats.sample_stats[sample_name].number_of_bases = assembly_sample_stats[:number_of_bases]
+ 
+    end
+    return assembly_run_stats
+  end
 end

data/lib/trim_and_correct.rb

@@ -23,29 +23,37 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
     `#{quake_path} -f quake_file_list.txt -k 15 -q #{quality_scale}`
   end
   sample_map.each do |sample_file_prefix, sample_name|
-    `perl /Volumes/NGS2_DataRAID/projects/MRSA/scripts/fastq-remove-orphans.pl -1 paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension} -2 paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}`
+    if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      `perl /Volumes/NGS2_DataRAID/projects/MRSA/scripts/fastq-remove-orphans.pl -1 paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension} -2 paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}`
+    end
   end
 
   # cleanup and rename files
+
   sample_map.each do |sample_file_prefix, sample_name|
-    system("rm #{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
-    system("rm #{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
-    system("rm paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
-    system("rm paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
-    system("rm orphaned_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
-    system("rm orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
-    system("rm error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt")
-    system("rm error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt")
-    system("rm paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt")
-    system("rm paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
-    system("rm paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt")
-    system("rm paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
-    system("rm paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-    system("rm paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
-    system("rm orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-    system("rm orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
-    system("mv paired_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension} #{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-    system("mv paired_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension} #{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+    File.delete("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+    File.delete("#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
+    File.delete("orphaned_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+    File.delete("orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
+    if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
+      File.delete("error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt")
+      File.delete("error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+      File.delete("orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      File.delete("orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+      File.rename("paired_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}", "#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      File.rename("paired_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}", "#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+    else
+      File.rename("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}", "#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+      File.rename("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}", "#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
+    end
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fastq-factory
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-24 00:00:00.000000000 Z
+date: 2012-08-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -165,7 +165,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2858636493634267725
+      hash: 2435527591364603339
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: