new_contents: import fnmatch
  import os
  import subprocess
  
  
  path_to_file= '/Volumes/Drobo/YX-chapman_rsem'
  
  gene_list = []
  iso_list = []
  for root, dirnames, filenames in os.walk(path_to_file):
      for f in filenames:
          if '.genes.results' in f:
              gpat = os.path.join(root,f)
              gene_list.append(gpat)
          if '.isoforms.results' in f:
              ipat = os.path.join(root,f)
              iso_list.append(ipat)
  
  subprocess.call('rsem-generate-data-matrix '+' '.join(gene_list)+' > '+os.path.basename(path_to_file)+'.gene.count.matrix',shell=True)
  subprocess.call('rsem-generate-data-matrix '+' '.join(iso_list)+' > '+os.path.basename(path_to_file)+'.iso.count.matrix',shell=True)
  
subject: build rsem matrix from many files