from-scratch now removes CIFs and annotations

persalteas · Jan 31, 2021 · e70f9e6 · e70f9e6
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commit e70f9e6
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diff --git a/KnownIssues.md b/KnownIssues.md
@@ -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.
+* Possibly, more metrics about the alignments coming from Infernal.
+* Move to SILVA LSU release 138
diff --git a/RNAnet.py b/RNAnet.py
@@ -1072,8 +1072,8 @@ def process_options(self):
             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",