old_contents: #!/usr/bin/env python
  
  import argparse
  
  __description__ = "Sorts secondary structre and sequence from PDB"
  __author__ = "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  __email__ = "malvika.sharan@uni-wuerzburg.de"
  
  
  parser = argparse.ArgumentParser()
  parser.add_argument(
      "-i", "--pdb_ss_file", help="input secondary structure")
  parser.add_argument(
      "-seq", "--pdb_seq_path", help="output pdb sequence")
  parser.add_argument(
      "-str", "--pdb_str_path", help="output pdb structure")
  args = parser.parse_args()
  
  
  "Sorts secondary structre and sequence from PDB"
  sequence_id_dict = {}
  out_seq_file = args.pdb_seq_path+'/pdb_sequence.txt'
  out_ss_file = args.pdb_str_path+'/pdb_secstr.txt'
      
  with open(args.pdb_ss_file) as in_fh:
      with open(out_seq_file, 'w') as out_seq_fh:
          with open(out_ss_file, 'w') as out_ss_fh:
              for data in in_fh.read().split('>'):
                  if "sequence" in data:
                      seq_id = data.split(':')[0]
                      sequence_id_dict[seq_id] = data
                      out_seq_fh.write('>%s' % data)
                  elif "secstr" in data:
                      str_id = data.split(':')[0]
                      data = data.replace(' ', '0')
                      seq_len = (len(sequence_id_dict[str_id]) - len(data))
                      for short in range(int(seq_len)):
                          data = data.strip()+'0'
                          out_ss_fh.write('>%s' % data)
  
new_contents: #!/usr/bin/env python
  # Description = Formt PDB secodary structure database
  # author= "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  # email = "malvika.sharan@uni-wuerzburg.de"
  # 2016-05-20
  
  import argparse
  
  __description__ = "Sorts secondary structre and sequence from PDB"
  __author__ = "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  __email__ = "malvika.sharan@uni-wuerzburg.de"
  
  
  parser = argparse.ArgumentParser()
  parser.add_argument(
      "-i", "--pdb_ss_file", help="input secondary structure")
  parser.add_argument(
      "-seq", "--pdb_seq_path", help="output pdb sequence")
  parser.add_argument(
      "-str", "--pdb_str_path", help="output pdb structure")
  args = parser.parse_args()
  
  
  "Sorts secondary structre and sequence from PDB"
  sequence_id_dict = {}
  out_seq_file = args.pdb_seq_path+'/pdb_sequence.txt'
  out_ss_file = args.pdb_str_path+'/pdb_secstr.txt'
      
  with open(args.pdb_ss_file) as in_fh:
      with open(out_seq_file, 'w') as out_seq_fh:
          with open(out_ss_file, 'w') as out_ss_fh:
              for data in in_fh.read().split('>'):
                  if "sequence" in data:
                      seq_id = data.split(':')[0]
                      sequence_id_dict[seq_id] = data
                      out_seq_fh.write('>%s' % data)
                  elif "secstr" in data:
                      str_id = data.split(':')[0]
                      data = data.replace(' ', '0')
                      seq_len = (len(sequence_id_dict[str_id]) - len(data))
                      for short in range(int(seq_len)):
                          data = data.strip()+'0'
                          out_ss_fh.write('>%s' % data)
  
subject: Update sort_sec_struc_pdb_data.py