def get_extended_sbol(db, part_id, rule = "RFC10"):
  user_part = db.getUserPart(part_id)
  print user_part
  table = user_part["part_type"]
  model_param = None
  if table != "Coding":
    model_param = db.select_with_name(table, user_part["Number"])
  component = json.loads(user_part["parts"])
  sys_comp = filter(lambda x: x[0:3] == "BBa", component)
  sys_comp = [find_file(x+".xml", ".") for x in sys_comp]
  content = union(rule, sys_comp)
  print content
  cnt = 0
  offset = 0
  intermediat = len(getattr(__import__("component_union"), rule).intermediat)
  for i in xrange(len(component)):
    if component[i][0:3] == "BBa":
      content[cnt]["seq"]["bioStart"] += offset
      content[cnt]["seq"]["bioEnd"] += offset
      cnt += 1
    else:
      offset += len(component[i])
      if i > 0:
        offset += intermediat
  header = extend(user_part, model_param)
  print component
  dna_sequence = get_new_part_sequence(component, rule)
  sbol = formatter_v11(content, dna_sequence, header)
  return sbol
Exemple #2
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def test():
  rule = "RFC25"
  content = component_union.union(rule, sys.argv[1:])
  # path = 'F:/igemgit/project/Python27/web/test/BBa_E1010.xml'
  # content = component_union.union(rule, path)
  dna_sequence = component_union.connect(rule, content)
  sbol = component_union.formatter_v11(content, dna_sequence)
  print sbol
  print sequence_serializer.format_to_json(sbol)