from-scratch now removes CIFs and annotations

@@ -20,4 +20,5 @@
 * [UPCOMING] Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
 * [UPCOMING] Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
 * A field estimating the quality of the sequence alignment in table family.
-* Possibly, more metrics about the alignments coming from Infernal.
\ No newline at end of file
+* Possibly, more metrics about the alignments coming from Infernal.
+* Move to SILVA LSU release 138
\ No newline at end of file

@@ -1072,8 +1072,8 @@ class Pipeline:
             elif opt == "--from-scratch":
                 warn("Deleting previous database and recomputing from scratch.")
                 subprocess.run(["rm", "-rf",
-                                # path_to_3D_data + "annotations",  # DEBUG : keep the annotations !
-                                # path_to_3D_data + "RNAcifs",      # DEBUG : keep the cifs !
+                                path_to_3D_data + "annotations",
+                                path_to_3D_data + "RNAcifs",
                                 path_to_3D_data + "rna_mapped_to_Rfam",
                                 path_to_3D_data + "rnaonly",
                                 path_to_seq_data + "realigned",