bio-ngs 0.3.2.alpha.01 → 0.4.2.alpha.01

data/lib/bio/ngs/utils.rb

@@ -22,6 +22,14 @@ module Bio
         end
       end
       class << self
+        
+        def parallel_exec(command_blocks)
+          command_blocks.each do |block|
+            fork(&block)
+          end
+          Process.waitall
+        end
+        
         def binary(name)
           begin
             if !(plugin_binaries_found = find_binary_files(name)).empty?
@@ -123,7 +131,7 @@ module Bio
               uncompress = uncompress_command(tool_record["suffix"])
               STDERR.puts "#{uncompress} #{tool_file_name}"
               system "#{uncompress} #{tool_file_name}"
-              STDERR.puts "sto per uscire"
+              STDERR.puts "completed."
               if Dir.exists?(tool_dir_name)
                 tool_dir_name
               elsif Dir.exists?("#{tool_name}-#{tool_record['version']}")
@@ -138,6 +146,8 @@ module Bio
               tool_dir_name = uncompress_any(tool_name, tool_record)
               puts "Compiling #{tool_name}..."
               cd(tool_dir_name) do
+                #system "#{tool_record["lib"]}='#{path_external}/bin/common/lib'" if tool_record["lib"]
+                #system "#{tool_record["flags"]}='-O2'" if tool_record["flags"]
                 system "PKG_CONFIG_PATH='#{path_external}/bin/common/lib/pkgconfig' ./configure --prefix=#{path_binary} --bindir=#{path_binary}"
                 system "make"
                 system "make install"

data/lib/bio-ngs.rb

@@ -44,6 +44,7 @@ require 'bio/appl/ngs/bowtie-inspect'
 require 'bio/appl/ngs/sff_extract'
 require 'bio/appl/ngs/bcl2qseq' #TODO: FIX THIS BUGGY CODE in THOR TASK
 
+require 'bio/appl/ngs/cufflinks/iterators'
 require 'bio/appl/ngs/cufflinks'
 require 'bio/appl/ngs/samtools'
 require 'bio/appl/ngs/fastx'

data/lib/tasks/convert.thor

@@ -419,6 +419,7 @@ module Convert
               method_option :min_fpkm, :type => :numeric, :aliases => "-f", :default=> 0.0, :desc => "Store a value if its fpkm is at least"
               method_option :z_scores, :type => :boolean, :aliases => "-z", :default=> false, :desc=> "Return a matrix of Z-scores other than fpkm"
               method_option :up, :type => :boolean, :aliases => '-u', :default => true, :desc => "Up regulated (true), down regulated (false)"
+              method_option :force_not_significative, :type=>:boolean, :aliases=>'n', :default=>false, :desc=>"consider not significan value dutin computation of signature."
               def gene(diff_file, gtf)
                 how_regulated = options.up ? :up : :down
                 Bio::Ngs::Cufflinks::Diff.genes(diff_file,
@@ -450,5 +451,20 @@ module Convert
           end #Illumina
 
 
+          desc "list2table list", "reorganize a list of pairs key value in a table of key values. Tabular is the default separator"
+          def list2table(list)
+            dict = Hash.new{|h,k| h[k]=[]}
+              File.open(ARGV[0],'r') do |f|
+              f.each_line do |l|
+                 key, value = l.split
+                 dict[key]<<value
+              end
+            end
+
+            dict.each_pair do |key, values|
+              puts "#{key} #{values.join('  ')}"
+            end
+          end
+
         end #Convert
         #  Add methods to Enumerable, which makes them available to Array

data/lib/tasks/pre.thor

@@ -0,0 +1,130 @@
+class Pre < Thor
+  
+  desc "filter [DIR(s)]", "Filter the data using Y/N flag in FastQ headers (Illumina). Search for fastq.gz files within directory(ies) passed."
+  method_option :compression, :type => :string, :default => "pigz"
+  method_option :cpu, :type => :numeric, :default => 4
+  def filter(dir)
+    folders = Dir.glob(dir)
+    cmd_blocks = []
+    folders.each do |folder|
+      Dir.glob(folder+"/*.fastq.gz").sort.each do |fastq|
+        Dir.mkdir(folder+"/filtered") unless Dir.exists? folder+"/filtered"
+        fastq = fastq.split("/")[-1]
+        cmd_blocks << -> {system("zcat #{folder+"/"+fastq} | grep -A 3 '^@.* [^:]*:N:[^:]*:' | grep -v '^\-\-'| #{options[:compression]} > #{folder}/filtered/#{fastq}")}
+        if cmd_blocks == options[:cpu]
+          Bio::Ngs::Utils.parallel_exec(cmd_blocks)
+          cmd_blocks = []
+        end
+      end
+    end
+    Bio::Ngs::Utils.parallel_exec(cmd_blocks)
+  end
+  
+  
+  desc "merge [file(s)]","Merge together fastQ files (accepts wildcards)"
+  method_option :compressed, :type => :boolean, :default => true
+  method_option :cpu, :type => :numeric, :default => 4
+  def merge(file)
+    files = Dir.glob(file).sort
+    cat = (options[:compressed]) ? "zcat" : "cat"
+    files.each do |file|
+      system("#{cat} #{file} >> merged_reads.fastq")
+    end
+  end
+  
+  desc "paired_merge [file(s)]","Merge together FastQ files while checking for correct pairing (accepts wildcards)"
+  method_option :compressed, :type => :boolean, :default => false
+  def paired_merge(file)
+    files = Dir.glob(file).sort.find_all {|f| f=~/_R1_/}
+    cat = (options[:compressed] == true) ? "zcat" : "cat"
+    files.each do |file|
+      r1 = file
+      r2 = file.gsub(/_R1_/,"_R2_")
+      if File.exists? r2
+        r1_count = count_reads(r1,compressed:options[:compressed])
+        r2_count = count_reads(r2,compressed:options[:compressed])
+        puts "Read count: #{r1_count} : #{r2_count} , #{file}"
+          if r1_count == r2_count
+            blocks = []
+            blocks << -> {system("#{cat} #{r1} >> R1_reads.fastq")}
+            blocks << -> {system("#{cat} #{r2} >> R2_reads.fastq")}
+            Bio::Ngs::Utils.parallel_exec(blocks)
+          else
+            raise RuntimeError "Error: files #{r1} and #{r2} do not have the same number of reads!"
+          end
+      else
+        puts "WARN: file #{r2} does not exist! Reads from #{r1} will be considered as singlets"
+        system("#{cat} #{r1} >> singlets_reads.fastq")
+      end  
+    end
+  end
+  
+  desc "uncompress [file(s)]","Uncompress multiple files in parallel (accepts wildcards)"
+  method_option :cpu, :type => :numeric, :default => 4
+  def uncompress(file)
+    files = Dir.glob(file).sort
+    blocks = []
+    files.each do |file|
+      blocks << -> {system("gunzip #{file}")}
+      if blocks.size == options[:cpu]
+        Bio::Ngs::Utils.parallel_exec(blocks)
+        blocks = []
+      end
+    end
+    Bio::Ngs::Utils.parallel_exec(blocks) 
+  end
+  
+  
+  desc "trim [file(s)]","Calulate quality profile and trim the all the reads using FastX (accepts wildcards)"
+  method_option :cpu, :type => :numeric, :default => 4
+  method_option :min_qual, :type => :numeric, :default => 20
+  def trim(file)
+    files = Dir.glob(file).sort
+    cmd_blocks = []
+    files.each do |file|
+      
+      block = -> do
+        invoke "quality:fastq_stats", [file], {output:file+".stats"}
+        trim_position = options[:read_length]
+        lines = File.read(file+".stats").split("\n")
+        if lines.size == 0
+		      raise RuntimeError, "Error in Quality Stats file! Check fastx_quality_stat output"
+	      end
+	      read_length = (lines.size) -1
+        lines[1..-1].each_with_index do |line,index|
+          if line.split("\t")[7].to_i <= options[:min_qual]
+            trim_position = index +1
+            break
+          end 
+        end
+        if trim_position == options[:read_length]
+          puts "WARN: no bases under quality cutoff. No trimming needed on #{file}"
+          FileUtils.cp file, file+".ready"
+        elsif trim_position < 25 
+            puts "WARN: Trimming on #{file} will produce reads that are too short. The file will be discarded, please check quality scores."
+        else
+          puts "Trimming on position #{trim_position} for #{file}"
+          trim = Bio::Ngs::Fastx::Trim.new
+          trim.params={trim:read_length-trim_position+1, input:file, output:file+".ready"}
+          trim.run
+        end
+      end
+      
+      cmd_blocks << block
+      
+      if cmd_blocks.size == options[:cpu]
+        Bio::Ngs::Utils.parallel_exec(cmd_blocks)
+        cmd_blocks = []
+      end
+    end
+    Bio::Ngs::Utils.parallel_exec(cmd_blocks)
+  end
+  
+  private
+  
+  def count_reads(file,opts = {compressed:false})
+    cat = (opts[:compressed] == true) ? "zcat" : "cat"
+    total = `#{cat} #{file} | wc -l`.to_i / 4
+  end
+  
+end

data/lib/tasks/quality.thor

@@ -19,14 +19,14 @@ class Quality < Thor
     Bio::Ngs::Graphics.draw_area(qual,options[:width],options[:height],options[:fileout],"Nucleotide","Quality Score")
   end
 
-  desc "trim FASTQ", "trim all the sequences"
+  desc "quality_trim FASTQ", "Trim all the sequences using quality information"
   #TODO: create a wrapper
   method_option :min_size, :type=>:numeric, :default=>20, :aliases => "-l", :desc=>"Minimum length - sequences shorter than this (after trimming)
                     will be discarded. Default = 0 = no minimum length."
   method_option :min_quality, :type=>:numeric, :default=>10, :aliases => "-t", :desc=>"Quality threshold - nucleotides with lower 
                                       quality will be trimmed (from the end of the sequence)."
   method_option :output, :type=>:string, :aliases => "-o", :desc => "Output file name"
-  def trim(fastq)
+  def quality_trim(fastq)
     output_file = options.output || fastq.gsub(/(.*)_(forward|reverse)(.*)/,'\1_trim_\2\3')
     if output_file==fastq
       output_file+="_trim"
@@ -36,13 +36,12 @@ class Quality < Thor
       invoke :fastq_stats, [fastq]
     end
     #TODO check the file in input exists
-    trim = Bio::Ngs::Fastx::Trim.new
+    trim = Bio::Ngs::Fastx::QualityTrim.new
     trim.params={min_size:options.min_size, min_quality:options.min_quality, input:fastq, output:output_file}
     trim.run
     invoke :fastq_stats, [output_file]
   end
   
-  
   desc "fastq_stats FASTQ", "Reports quality of FASTQ file"
   method_option :output, :type=>:string, :aliases =>"-o", :desc => "Output file name. default is input file_name with .txt."
   def fastq_stats(fastq)

data/lib/tasks/rna.thor

@@ -14,7 +14,8 @@ class Rna < Thor
       wrapper.run :arguments=>[index, fastq_files ].flatten, :separator=>"="
 
       accepted_hits_bam_fn = File.join(outputdir, "accepted_hits.bam")
-      task.invoke "convert:bam:sort", [accepted_hits_bam_fn] # call the sorting procedure.
+      #DEPRECATED tophat sort data by default 
+      #task.invoke "convert:bam:sort", [accepted_hits_bam_fn] # call the sorting procedure.
   end
 
   desc "quant GTF OUTPUTDIR BAM ", "Genes and transcripts quantification"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ngs
 version: !ruby/object:Gem::Version
-  version: 0.3.2.alpha.01
+  version: 0.4.2.alpha.01
   prerelease: 6
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-10-10 00:00:00.000000000Z
+date: 2012-02-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2170881740 !ruby/object:Gem::Requirement
+  requirement: &2157120300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2170881740
+  version_requirements: *2157120300
 - !ruby/object:Gem::Dependency
   name: bio-bwa
-  requirement: &2170874980 !ruby/object:Gem::Requirement
+  requirement: &2157119680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,21 +33,21 @@ dependencies:
         version: 0.2.2
   type: :runtime
   prerelease: false
-  version_requirements: *2170874980
+  version_requirements: *2157119680
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2170868580 !ruby/object:Gem::Requirement
+  requirement: &2157119100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.0
+        version: 0.3.2
   type: :runtime
   prerelease: false
-  version_requirements: *2170868580
+  version_requirements: *2157119100
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2170865400 !ruby/object:Gem::Requirement
+  requirement: &2157118540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.14.6
   type: :runtime
   prerelease: false
-  version_requirements: *2170865400
+  version_requirements: *2157118540
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2170863100 !ruby/object:Gem::Requirement
+  requirement: &2157117900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
         version: 0.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *2170863100
+  version_requirements: *2157117900
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2170860560 !ruby/object:Gem::Requirement
+  requirement: &2157133620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
         version: 1.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *2170860560
+  version_requirements: *2157133620
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2170857700 !ruby/object:Gem::Requirement
+  requirement: &2157133000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,10 +88,10 @@ dependencies:
         version: 1.0.1
   type: :runtime
   prerelease: false
-  version_requirements: *2170857700
+  version_requirements: *2157133000
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2170855960 !ruby/object:Gem::Requirement
+  requirement: &2157132300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
         version: 3.0.5
   type: :runtime
   prerelease: false
-  version_requirements: *2170855960
+  version_requirements: *2157132300
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2170854340 !ruby/object:Gem::Requirement
+  requirement: &2157131680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
         version: 1.3.3
   type: :runtime
   prerelease: false
-  version_requirements: *2170854340
+  version_requirements: *2157131680
 - !ruby/object:Gem::Dependency
   name: bio-blastxmlparser
-  requirement: &2170851720 !ruby/object:Gem::Requirement
+  requirement: &2157131060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2170851720
+  version_requirements: *2157131060
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &2170848640 !ruby/object:Gem::Requirement
+  requirement: &2157130440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -132,10 +132,21 @@ dependencies:
         version: 0.9.0
   type: :runtime
   prerelease: false
-  version_requirements: *2170848640
+  version_requirements: *2157130440
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: &2157129820 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - =
+      - !ruby/object:Gem::Version
+        version: 0.9.2.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *2157129820
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2170844080 !ruby/object:Gem::Requirement
+  requirement: &2157129080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -143,10 +154,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2170844080
+  version_requirements: *2157129080
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2170840920 !ruby/object:Gem::Requirement
+  requirement: &2157128200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -154,10 +165,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2170840920
+  version_requirements: *2157128200
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2170839560 !ruby/object:Gem::Requirement
+  requirement: &2157127280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -165,21 +176,21 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *2170839560
+  version_requirements: *2157127280
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2170838040 !ruby/object:Gem::Requirement
+  requirement: &2157126720 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.9.11
   type: :development
   prerelease: false
-  version_requirements: *2170838040
+  version_requirements: *2157126720
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2170836560 !ruby/object:Gem::Requirement
+  requirement: &2157473200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -187,10 +198,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2170836560
+  version_requirements: *2157473200
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2170834960 !ruby/object:Gem::Requirement
+  requirement: &2157472260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -198,10 +209,10 @@ dependencies:
         version: 0.14.6
   type: :development
   prerelease: false
-  version_requirements: *2170834960
+  version_requirements: *2157472260
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2170831480 !ruby/object:Gem::Requirement
+  requirement: &2157471560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -209,10 +220,10 @@ dependencies:
         version: 1.0.6
   type: :development
   prerelease: false
-  version_requirements: *2170831480
+  version_requirements: *2157471560
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2170828140 !ruby/object:Gem::Requirement
+  requirement: &2157470260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -220,10 +231,10 @@ dependencies:
         version: 0.5.0
   type: :development
   prerelease: false
-  version_requirements: *2170828140
+  version_requirements: *2157470260
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2170826120 !ruby/object:Gem::Requirement
+  requirement: &2157468020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -231,10 +242,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *2170826120
+  version_requirements: *2157468020
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2170824340 !ruby/object:Gem::Requirement
+  requirement: &2157467300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -242,21 +253,21 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *2170824340
+  version_requirements: *2157467300
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2170822080 !ruby/object:Gem::Requirement
+  requirement: &2157465240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.0
+        version: 0.3.2
   type: :development
   prerelease: false
-  version_requirements: *2170822080
+  version_requirements: *2157465240
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2170819520 !ruby/object:Gem::Requirement
+  requirement: &2157480640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -264,10 +275,10 @@ dependencies:
         version: 1.0.1
   type: :development
   prerelease: false
-  version_requirements: *2170819520
+  version_requirements: *2157480640
 - !ruby/object:Gem::Dependency
   name: bio-bwa
-  requirement: &2170816740 !ruby/object:Gem::Requirement
+  requirement: &2157479520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -275,10 +286,10 @@ dependencies:
         version: 0.2.2
   type: :development
   prerelease: false
-  version_requirements: *2170816740
+  version_requirements: *2157479520
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2170814180 !ruby/object:Gem::Requirement
+  requirement: &2157478880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -286,10 +297,10 @@ dependencies:
         version: 3.0.5
   type: :development
   prerelease: false
-  version_requirements: *2170814180
+  version_requirements: *2157478880
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2170805160 !ruby/object:Gem::Requirement
+  requirement: &2157477800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -297,10 +308,10 @@ dependencies:
         version: 1.3.3
   type: :development
   prerelease: false
-  version_requirements: *2170805160
+  version_requirements: *2157477800
 - !ruby/object:Gem::Dependency
   name: bio-blastxmlparser
-  requirement: &2170803260 !ruby/object:Gem::Requirement
+  requirement: &2157476620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -308,10 +319,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2170803260
+  version_requirements: *2157476620
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &2170801680 !ruby/object:Gem::Requirement
+  requirement: &2157475400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -319,10 +330,10 @@ dependencies:
         version: 0.9.0
   type: :development
   prerelease: false
-  version_requirements: *2170801680
+  version_requirements: *2157475400
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &2170800800 !ruby/object:Gem::Requirement
+  requirement: &2157473980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -330,7 +341,18 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2170800800
+  version_requirements: *2157473980
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: &2157626640 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - =
+      - !ruby/object:Gem::Version
+        version: 0.9.2.2
+  type: :development
+  prerelease: false
+  version_requirements: *2157626640
 description: bio-ngs provides a framework for handling NGS data with BioRuby
 email: francesco.strozzi@gmail.com
 executables:
@@ -356,6 +378,7 @@ files:
 - lib/bio/appl/ngs/blast.rb
 - lib/bio/appl/ngs/bowtie-inspect.rb
 - lib/bio/appl/ngs/cufflinks.rb
+- lib/bio/appl/ngs/cufflinks/iterators.rb
 - lib/bio/appl/ngs/fastx.rb
 - lib/bio/appl/ngs/samtools.rb
 - lib/bio/appl/ngs/sff_extract.rb
@@ -390,6 +413,7 @@ files:
 - lib/tasks/history.thor
 - lib/tasks/homology.thor
 - lib/tasks/ontology.thor
+- lib/tasks/pre.thor
 - lib/tasks/project.thor
 - lib/tasks/quality.thor
 - lib/tasks/rna.thor
@@ -431,7 +455,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1963233679841043858
+      hash: 4413176982890419271
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -440,7 +464,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: bio-ngs provides a framework for handling NGS data with BioRuby