text: import sys
  from pyspark import SparkConf, SparkContext
  import datetime
  
  APP_NAME = "hmmer-spark testing"
  
  def main(sc,filename):
  
      a = datetime.datetime.now()
      scriptPath = "hmmer.sh"
   
      # small dataset
      a = datetime.datetime.now()
      #data = sc.textFile(filename).repartition(3)
      data = sc.textFile(filename) 
      pipeRDD = data.pipe(scriptPath)
      pipeRDD.collect()
      b = datetime.datetime.now()
      print "**** %s ***" % filename
      print " "
      print (b-a)
      print " "
      print "************************************************************"
  
  if __name__ == "__main__":
      conf = SparkConf().setAppName(APP_NAME)
      conf = conf.setMaster("local[*]")
      sc   = SparkContext(conf=conf)
      filename = str(sys.argv[1])
      main(sc,filename)
      sc.stop()
  