Module: Bio::Ngs::Cufflinks::Utils::ClassMethods

Defined in:
lib/bio/appl/ngs/cufflinks/iterators.rb

Instance Method Summary collapse

Instance Method Details

#add_iterator_for(type_file_name, opts = {}) ⇒ Object

Create an iterator using the specified type_name file. in case of Cufflinks type_file_name can be gene,isoform, cds, tss_group



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# File 'lib/bio/appl/ngs/cufflinks/iterators.rb', line 17

def add_iterator_for( type_file_name, opts={})
  plural_name = type_file_name = type_file_name.to_s
  if %w(genes isoforms cds tss_groups).include?(type_file_name)
    type_file_name=type_file_name[0..-2] if type_file_name!="cds"
    self.class.send  :define_method, "foreach_#{type_file_name}_tracked" do |path = '.', &block|
      file_name = File.join(path,"#{plural_name}.fpkm_tracking")
      CSV.foreach(file_name, headers: true, converters: :numeric, col_sep:"\t") do |data|
        block.call(data)
      end #cvs_foreach
    end #define_method
 else
    raise "#{type_file_name} is not a valid base name for cuffdiff's output, must be plural and in this set: genes, cds, isoforms, tss_groups"
 end #if
end