new_contents: #!/usr/bin/env python
  __author__ = 'Guanwen Wang'
  
  # Guanwen Not part of the final project
  import sys, os, fnmatch
  
  # get Assembly for the single and pair ended genomes
  
  # color class to highlight the warnings
  class bcolors:
      HEADER = '\033[95m'
      OKBLUE = '\033[94m'
      OKGREEN = '\033[92m'
      WARNING = '\033[93m'
      FAIL = '\033[91m'
      ENDC = '\033[0m'
      MAGENTA = "\033[.35m"
      ENDCODE = "\033[.0m"
  
  PrintAll = 0
  
  TotalFound = 0
  result = []
  
  HHListS = 'HHListS.txt'
  HHListP = 'HHListSingleP.txt'
  
  pathArr = ['/thomas1/mcbs913/shared_data1/datasets/reads']
  patternS = 'Ha*-s*10.*'
  #patternP = 'Ha*-*-*-*-10-*-*'
  patternP = 'Ha*-*-*-*-10-*-1.*'
  
  def GenomeFilter(pattern, pathArr):
      global result 
      global TotalFound
      for path in pathArr:
          for root, dirs, files in os.walk(path):
              found = False
              for name in files:
                  if fnmatch.fnmatch(name, pattern):
                      found = True
                      targetFile = os.path.join(root, name)
                      if PrintAll == 1:
                          print targetFile
  		    TotalFound += 1
                      result.append(targetFile)
              if( found == False):
                  print root 
                  print bcolors.FAIL + "WARNING: No Genome files found\n" + bcolors.ENDC
     
  
  
  GenomeFilter(patternS, pathArr)
  result.sort()
  
  with open(HHListS, 'w') as f:
      for s in result:
          f.write(s + '\n');
  
  if PrintAll == 1:
     print TotalFound
     print result
  
  TotalFound = 0
  del result[:]
  
  GenomeFilter(patternP, pathArr)
  result.sort()
  
  with open(HHListP, 'w') as f:
      for s in result:
          f.write(s + '\n');
  
  if PrintAll == 1:
     print TotalFound
     print result
  
subject: Create getAssemblyList.py