old_contents: #!/usr/bin/env python
  # Description = Merges domains files selected from CDD and InterPro
  # author= "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  
  import os
  import sys
  
  cdd_domains = sys.argv[1]
  ipr_domains = sys.argv[2]
  merged_file = sys.argv[3]
  
  with open(merged_file, 'w') as out_fh:
      header = '\t'.join(['ReferenceId', 'DomainId',
                          'ShortName', 'FullName',
                          'Members', 'Length', 'SelectionTerm'])+'\n'
      out_fh.write(header)
      if os.path.exists(cdd_domains):
          with open(cdd_domains, 'r') as cdd_fh:
              out_fh.write(cdd_fh.read()+'\n')
      if os.path.exists(ipr_domains):
          with open(ipr_domains, 'r') as ipr_fh:
              out_fh.write(ipr_fh.read()+'\n')
  
new_contents: #!/usr/bin/env python
  # Description = Merges domains files selected from CDD and InterPro
  
  import os
  import sys
  
  
  def merge_domain_data(cdd_domains, ipr_domains, merged_file):
      with open(merged_file, 'w') as out_fh:
          header = '\t'.join(['ReferenceId', 'DomainId',
                              'ShortName', 'FullName',
                              'Members', 'Length', 'SelectionTerm'])+'\n'
          out_fh.write(header)
          if os.path.exists(cdd_domains):
              with open(cdd_domains, 'r') as cdd_fh:
                  out_fh.write(cdd_fh.read()+'\n')
          if os.path.exists(ipr_domains):
              with open(ipr_domains, 'r') as ipr_fh:
                  out_fh.write(ipr_fh.read()+'\n')
  
  if __name__ == '__main__':
      cdd_domains = sys.argv[1]
      ipr_domains = sys.argv[2]
      merged_file = sys.argv[3]
      merge_domain_data(cdd_domains, ipr_domains, merged_file)
  
subject: Update compile_selected_domains.py