old_contents: # acsn2hugo.py -- Convert ACSN gene to HUGO gene
  #
  # jean-daniel.granet@mines-paristech.fr
  
  import sys
  import argparse
  
  def main():
      # get arguments : 
      parser = argparse.ArgumentParser(description='Convert ACSN gene to HUGO gene')
      parser.add_argument('acsn', help='ACSN to convert in .sif format')
      parser.add_argument('curated', help='reference file in gmt format')
      parser.add_argument('hugo', help='HUGO file to create')
      args = parser.parse_args()
      
      curated = dict()
      # read the curated file and save into a dictionary :
      # the key is the acsn gene name and the value is the hugo gene name
      with open(args.curated, 'r') as fdCurated:
          for line in fdCurated:
              line_split = line.split('\tna\t')
              curated[line_split[0].strip()] = line_split[1].strip()
          fdCurated.close()
      # read the acsn network file and write the corresponding hugo network into the output file
      with open(args.acsn, 'r') as fdAcsn:
          with open(args.hugo, 'w') as fdHugo:
              for line in fdAcsn:
                  line_split = line.split('\t')
                  geneA = curated[line_split[0].strip()].split()
                  geneB = curated[line_split[2].strip()].split()
                  for elemA in geneA:
                      for elemB in geneB:
                          fdHugo.write("%s\n" % "\n".join(["%s %s %s" % (elemA, line_split[1], elemB)]))
              fdHugo.close()
          fdAcsn.close() 
  
  if __name__ == "__main__":
      main()
  
new_contents: # acsn2hugo.py -- Convert ACSN gene to HUGO gene
  #
  # jean-daniel.granet@mines-paristech.fr
  
  import sys
  import argparse
  
  def main():
      # get arguments : 
      parser = argparse.ArgumentParser(description='Convert ACSN gene to HUGO gene')
      parser.add_argument('acsn', help='ACSN to convert in .sif format')
      parser.add_argument('curated', help='reference file in gmt format')
      parser.add_argument('hugo', help='HUGO file to create')
      args = parser.parse_args()
      
      curated = dict()
      # read the curated file and save into a dictionary :
      # the key is the acsn gene name and the value is the hugo gene name
      # curated [ "acsn entity name" ] = "hugo\tgene\tnames\tin\tthe\tacsn\tentity"
      with open(args.curated, 'r') as fdCurated:
          for line in fdCurated:
              line_split = line.split('\tna\t')
              curated[line_split[0].strip()] = line_split[1].strip()
          fdCurated.close()
  
      # read the acsn network file and write the corresponding hugo network into the output file
      with open(args.acsn, 'r') as fdAcsn:
          with open(args.hugo, 'w') as fdHugo:
              for line in fdAcsn:
                  line_split = line.split('\t')
                  geneA = curated[line_split[0].strip()].split()
                  geneB = curated[line_split[2].strip()].split()
                  for elemA in geneA:
                      for elemB in geneB:
                          fdHugo.write("%s\n" % "\n".join(["%s %s %s" % (elemA, line_split[1], elemB)]))
              fdHugo.close()
          fdAcsn.close() 
  
  if __name__ == "__main__":
      main()
  
subject: Add infos about the structure of dict curated