CuffDiff output iterator, preliminar example

gistfile1.rb

#CLASS DEFINITION Bio::Ngs::Cufflinks
      class Diff
        include Bio::Command::Wrapper
        include Bio::Ngs::Cufflinks::Diff::Utils

        set_program Bio::Ngs::Utils.binary("cuffdiff")

        add_option "output-dir", :type => :string, :aliases => '-o', :default => "./"
        add_option "time-series", :type => :boolean, :aliases => '-T'
        add_option "min-alignment-count", :type => :numeric, :aliases => '-c'
        add_option "FDR", :type => :numeric, :aliases => '-F'
        #TODO:FIX        add_option "mask-file", :type => :string, :aliases => '-M'
        #TODO:FIX        add_option "frag-bias-correct", :type => 
        add_option "multi-read-correct", :type => :boolean, :aliases => '-u'
        add_option "upper-quartile-norm", :type => :boolean, :aliases => 'N'
        add_option "labels", :type => :array, :aliases => '-L'
        add_option "num-threads", :type => :numeric, :aliases => '-p'
        add_option "library-type", :type => :string, :aliases => '-l'
        add_option "frag-len-mean", :type => :numeric, :aliases => '-m'
        add_option "frag-len-std-dev", :type => :numeric, :aliases => '-s'
        add_option "num-importance-samples", :type => :numeric, :aliases => '-i'
        add_option "max-mle-iterations", :type => :numeric, :aliases => '-e'
        add_option "compatible-hits-norm", :type => :boolean, :aliases => '-h'
        add_option "total-hits-norm", :type => :boolean, :aliases => '-t'
        add_option "poisson-dispersion", :type => :boolean, :aliases => '-d'
        add_option "verbose", :type => :boolean, :aliases => '-v'
        add_option "quiet", :type => :boolean, :aliases => '-q'
        add_option "no-update-check", :type => :boolean, :aliases => '-j'
        add_option "emit-count-tables", :type => :boolean, :aliases => '-b'
        
        #define iterators
        add_iterator_for :genes
        add_iterator_for :isoforms
        add_iterator_for :cds
        add_iterator_for :tss_groups
end #Diff

#HOW TO USE THE functionality

    Bio::Ngs::Cufflinks::Diff.foreach_gene_tracked("path_to_cuffdiff_output_directory") do |gene_fpkm_track|
      expression_profile = (1..7).map do |sample_idx|
        gene_fpkm_track["q#{sample_idx}_FPKM"].to_f
      end
      
      #do your stuff accessing this tabular file with gene_fpkm_track["name of the field"]
    end