Module: BioRdf::Parsers::BroadGSEA::Parser

Includes:
Bio::Log
Defined in:
lib/bio-rdf/parsers/gsea/broadgsea.rb

Class Method Summary collapse

Class Method Details

.do_parse(input, filter, output) ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 129

def Parser::do_parse input, filter, output
  log = LoggerPlus.new 'gsea'
  log.level = INFO
  log.outputters = Outputter.stderr
  log.warn("Fetching "+input)
  print "Marker\tGenotype\tGS\tSIZE\tSOURCE\tES\tNES\tNOM p-val\tFDR q-val\tFWER p-val\tTag \%\tGene \%\tSignal\tFDR (median)\tglob.p.val\n"
  Dir.foreach(input) do |entry| # two step search, because of many dirs
    next if entry == '.' or entry == '..'
    log.info("Parsing directory "+entry)
    clsfilename = File.join(input,entry,"*cls")
    clsfilename = Dir.glob(clsfilename)
    raise "We need one cls file: #{clsfilename}" if clsfilename.size != 1
    clsfilename = clsfilename[0]
    # log.info(resultfilenames)
    resultfilenames = File.join(input,entry,"*SUMMARY.RESULTS.REPORT.[01].txt")
    Dir.glob(resultfilenames) do |fn|
      genotype = "A"
      genotype = "B" if fn =~ /1.txt/
      marker = "unknown"
      # fetch marker name
      if File.exist?(clsfilename)
        cls = BioRdf::Parsers::BroadGSEA::ParseClsRecord.new(File.read(clsfilename))
        marker = cls.classnames[0]
      end
      gsea_results = BioRdf::Parsers::BroadGSEA::ParseResultFile.new(fn)
      recs = gsea_results.find_all { | rec | rec.fdr_q_value <= 0.25 }
      recs.each do | rec |
        print "#{marker}\t#{genotype}\t"+rec.to_list.join("\t"),"\n"
      end
    end
  end
end

.handle_options ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 98

def Parser::handle_options 
  options = OpenStruct.new()
  
  opts = OptionParser.new() do |o|
    o.banner = "Usage: #{File.basename($0)} gsea [options] dir"

    o.on_tail("-h", "--help", "Show help and examples") {
      print(o)
      exit()
    }
    o.on("-e filter","--exec filter",String, "Execute filter") do |s|
      options.exec = s
    end

    o.on("--tabulate","Output tab delimited table") do
      options.output = :tabulate
    end

  end
  opts.parse!(ARGV)
  dir = ARGV[0]
  if dir and File.directory?(dir)
    do_parse(dir, options.exec, options.output)
  else
    raise "you should supply a GSEA directory!" 
  end
end