Whenever I query DAFT_direction with a lineage that is not in the species tree the code crashes due to the following part of the code:
def dji_output_name(self,out_filec,sp_string,lineage1,lineage2):
node_map,branch_map,sp_labeled = self.id_it(sp_string)
lineage1_id = self.map_id_tag(lineage1,sp_labeled)
lineage2_id = self.map_id_tag(lineage2,sp_labeled)
if lineage1_id is None:
lineage1_id = self.short_output_token(lineage1)
if lineage2_id is None:
lineage2_id = self.short_output_token(lineage2)
return str(out_filec) + "_" + str(lineage1_id) + "_" + str(lineage2_id)
Whenever I query DAFT_direction with a lineage that is not in the species tree the code crashes due to the following part of the code:
As th lineage_id equals None and the function
self.short_output_token()is not defined.