def plasmid_sbol(db, groups, rule="RFC10"):
circuit = groups["circuit"]
copy = groups["copy"]
components = []
sequence = ""
offset = 0
plasmid_backbone = db.getPlasmidBackboneNearValue(copy)["Number"]
circuit[-1]["sbol"].append({"type": "PlasmidBackbone", "name": plasmid_backbone})
for data in circuit:
comp_names = [cc["name"] for cc in data["sbol"]]
file_list = [find_file(s + ".xml", ".") for s in comp_names]
sbol = component_union.get_sbol(file_list, rule)
sbol2 = format_to_json(sbol)
idx = 0
for item in sbol2["DnaComponent"]["annotations"]:
tmp = item["SequenceAnnotation"]
tmp["subComponent"]["DnaComponent"]["type"] = data["sbol"][idx]["type"]
tmp["bioStart"] = str(int(tmp["bioStart"]) + offset)
tmp["bioEnd"] = str(int(tmp["bioEnd"]) + offset)
idx += 1
offset += len(sbol2["DnaComponent"]["DnaSequence"]["nucleotides"])
components += sbol2["DnaComponent"]["annotations"]
if data["state"] == "trans":
sequence += trans(sbol2["DnaComponent"]["DnaSequence"]["nucleotides"])
else:
sequence += sbol2["DnaComponent"]["DnaSequence"]["nucleotides"]
sbol2["DnaComponent"]["annotations"] = components
sbol2["DnaComponent"]["DnaSequence"]["nucleotides"] = sequence
return sbol2
def getPlasmidSbol_deprecated(self, message): sbol = component_union.get_sbol(message["component"], rule) ret = format_to_json(sbol) return ret