old_contents: #!/usr/bin/env python 
  
  __description__ = ""
  __author__ = "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  __email__ = "malvika.sharan@uni-wuerzburg.de"
  __version__ = ""
  
  import os       
  import sys
  import argparse
  
  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()
  
  def main():
      "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)
                              
  if __name__ == '__main__':
      
      main()   
  
new_contents: #!/usr/bin/env python 
  
  import os       
  import sys
  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()
  
  def main():
      "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)
                              
  if __name__ == '__main__':
      
      main()   
  
subject: Update sort_sec_struc_pdb_data.py