bug quoted_node_names in SO

Author: sinamajidian

FastOMA/_utils_frag_SO_detection.py

@@ -370,7 +370,7 @@ def handle_fragment_msa(prot_dubious_msa_list, seq_dubious_msa_list, gene_tree,
                 (msa_filt_row_col_new, msa_filt_col, hogs_children_level_list) = _utils_subhog.filter_msa(merged_msa_new, genetree_msa_file_addr+"_merged", hogs_children_level_list)
             if len(msa_filt_row_col_new) > 1 and len(msa_filt_row_col_new[0]) > 3:
                 gene_tree_raw = _wrappers.infer_gene_tree(msa_filt_row_col_new, genetree_msa_file_addr+"_merged_")
-                gene_tree = Tree(gene_tree_raw + ";", format=0)
+                gene_tree = Tree(gene_tree_raw , format=0, quoted_node_names=True) #+ ";"
             else:
                 gene_tree = ""
                 # fragments_remove_list += fragments_list_remove # for now fragments_list_remove include 1 prots