Class: Bio::Ngs::Cufflinks::QuantificationDenovo

Inherits:
Quantification show all
Defined in:
lib/bio/appl/ngs/cufflinks.rb

Instance Method Summary collapse

Methods included from Utils

included

Methods included from Command::Wrapper

#class_name, #default_options, included, #initialize, #normalize_params, #options, #options=, #output, #params, #params=, #path, #path=, #pipe_ahead, #pipe_ahead=, #pipe_ahead?, #program, #reset_params, #run, #sub_program, #thor_task, #to_cmd_ary, #use_aliases?

Instance Method Details

#get_new_transcripts(file = nil, type = "gtf") ⇒ Object

returns new trascripts from a gff3 file, it creates the file if doesn’t exist gets only the brand new.



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 151

def get_new_transcripts(file=nil, type="gtf")
  # TODO implement conversion to gff3
  file||= "transcripts.#{type}"
  # if type=="gtf"
  # unless File.exists?(file)
  #   to_gff3(File.dirname(File.absolute_path(file)))
  # end
  File.open()
end