More command line options

@@ -210,7 +210,7 @@ class Chain:
         notify(status)
         notify(status)
 
 
     @trace_unhandled_exceptions
     @trace_unhandled_exceptions
-    def extract_3D_data(self):
+    def extract_3D_data(self, save_logs=True):
         """ Maps DSSR annotations to the chain. """
         """ Maps DSSR annotations to the chain. """
 
 
         ############################################
         ############################################
@@ -513,7 +513,7 @@ class Chain:
             return None
             return None
 
 
         # Log chain info to file
         # Log chain info to file
-        if self.mapping is not None:
+        if save_logs and self.mapping is not None:
             self.mapping.to_file(self.chain_label+".log")
             self.mapping.to_file(self.chain_label+".log")
 
 
         return df
         return df
@@ -982,6 +982,7 @@ class Pipeline:
         self.REUSE_ALL = False
         self.REUSE_ALL = False
         self.SELECT_ONLY = None
         self.SELECT_ONLY = None
         self.ARCHIVE = False
         self.ARCHIVE = False
+        self.SAVELOGS = True
 
 
     def process_options(self):
     def process_options(self):
         """Sets the paths and options of the pipeline"""
         """Sets the paths and options of the pipeline"""
@@ -992,7 +993,7 @@ class Pipeline:
             opts, _ = getopt.getopt( sys.argv[1:], "r:hs", 
             opts, _ = getopt.getopt( sys.argv[1:], "r:hs", 
                                     [   "help", "resolution=", "keep-hetatm=", "from-scratch",
                                     [   "help", "resolution=", "keep-hetatm=", "from-scratch",
                                         "fill-gaps=", "3d-folder=", "seq-folder=",
                                         "fill-gaps=", "3d-folder=", "seq-folder=",
-                                        "no-homology", "ignore-issues", "extract", "only=", "all",
+                                        "no-homology", "ignore-issues", "extract", "only=", "all", "no-logs",
                                         "archive", "update-homologous" ])
                                         "archive", "update-homologous" ])
         except getopt.GetoptError as err:
         except getopt.GetoptError as err:
             print(err)
             print(err)
@@ -1035,6 +1036,7 @@ class Pipeline:
                 print("--update-homologous\t\tRe-download Rfam and SILVA databases, realign all families, and recompute all CSV files")
                 print("--update-homologous\t\tRe-download Rfam and SILVA databases, realign all families, and recompute all CSV files")
                 print("--from-scratch\t\t\tDelete database, local 3D and sequence files, and known issues, and recompute.")
                 print("--from-scratch\t\t\tDelete database, local 3D and sequence files, and known issues, and recompute.")
                 print("--archive\t\t\tCreate a tar.gz archive of the datapoints text files, and update the link to the latest archive")
                 print("--archive\t\t\tCreate a tar.gz archive of the datapoints text files, and update the link to the latest archive")
+                print("--no-logs\t\t\tDo not save per-chain logs of the numbering modifications")
                 print()
                 print()
                 print("Typical usage:")
                 print("Typical usage:")
                 print(f"nohup bash -c 'time {runDir}/RNAnet.py --3d-folder ~/Data/RNA/3D/ --seq-folder ~/Data/RNA/sequences -s --archive' &") 
                 print(f"nohup bash -c 'time {runDir}/RNAnet.py --3d-folder ~/Data/RNA/3D/ --seq-folder ~/Data/RNA/sequences -s --archive' &") 
@@ -1096,6 +1098,8 @@ class Pipeline:
                 self.EXTRACT_CHAINS = True
                 self.EXTRACT_CHAINS = True
             elif opt == "--archive":
             elif opt == "--archive":
                 self.ARCHIVE = True
                 self.ARCHIVE = True
+            elif opt == "--no-logs":
+                self.SAVELOGS = False
 
 
         if self.HOMOLOGY and "tobedefinedbyoptions" in [path_to_3D_data, path_to_seq_data] or path_to_3D_data == "tobedefinedbyoptions":
         if self.HOMOLOGY and "tobedefinedbyoptions" in [path_to_3D_data, path_to_seq_data] or path_to_3D_data == "tobedefinedbyoptions":
             print("usage: RNANet.py --3d-folder path/where/to/store/chains --seq-folder path/where/to/store/alignments")
             print("usage: RNANet.py --3d-folder path/where/to/store/chains --seq-folder path/where/to/store/alignments")
@@ -1227,7 +1231,7 @@ class Pipeline:
                 c.delete_me = False # give a second chance
                 c.delete_me = False # give a second chance
             if (c.chain_label not in self.known_issues) or not self.USE_KNOWN_ISSUES:
             if (c.chain_label not in self.known_issues) or not self.USE_KNOWN_ISSUES:
                 joblist.append(Job(function=work_build_chain, how_many_in_parallel=int(coeff_ncores*ncores), 
                 joblist.append(Job(function=work_build_chain, how_many_in_parallel=int(coeff_ncores*ncores), 
-                                    args=[c, self.EXTRACT_CHAINS, self.KEEP_HETATM, retry]))
+                                    args=[c, self.EXTRACT_CHAINS, self.KEEP_HETATM, retry, self.SAVELOGS]))
         try:
         try:
             results = execute_joblist(joblist)
             results = execute_joblist(joblist)
         except:
         except:
@@ -1957,7 +1961,7 @@ def work_mmcif(pdb_id):
     return 0
     return 0
 
 
 @trace_unhandled_exceptions
 @trace_unhandled_exceptions
-def work_build_chain(c, extract, khetatm, retrying=False):
+def work_build_chain(c, extract, khetatm, retrying=False, save_logs=True):
     """Reads information from JSON and save it to database.
     """Reads information from JSON and save it to database.
     If asked, also extracts the 3D chains from their original structure files.
     If asked, also extracts the 3D chains from their original structure files.
 
 
@@ -1969,7 +1973,7 @@ def work_build_chain(c, extract, khetatm, retrying=False):
     
     
     # extract the 3D descriptors
     # extract the 3D descriptors
     if not c.delete_me:
     if not c.delete_me:
-        df = c.extract_3D_data()
+        df = c.extract_3D_data(save_logs)
         c.register_chain(df)
         c.register_chain(df)
 
 
     # Small check
     # Small check