integration details

@@ -1200,11 +1200,13 @@ class Pipeline:
         # Check for a list of known problems:
         if os.path.isfile(runDir + "/known_issues.txt"):
             with open(runDir + "/known_issues.txt", 'r') as issues:
-                self.known_issues = [x[:-1] for x in issues.readlines()]
+                if self.HOMOLOGY:
+                    self.known_issues = [ x[:-1] for x in issues.readlines() if '-' in x ]
+                else:
+                    self.known_issues = [ x[:-1] for x in issues.readlines() id not '-' in x ]
             if self.USE_KNOWN_ISSUES:
                 print("\t> Ignoring known issues:")
-                for x in self.known_issues:
-                    print("\t  ", x)
+                print(" ".join(self.known_issues")
 
         if self.HOMOLOGY:
             # Ask Rfam if some are mapped to Rfam families
@@ -1560,6 +1562,7 @@ class Pipeline:
         if self.ARCHIVE:
             os.makedirs(runDir + "/archive", exist_ok=True)
             datestr = time.strftime('%Y%m%d')
+            subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
             subprocess.run(["tar", "-C", path_to_3D_data + "/datapoints", "-czf", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", "."])
             subprocess.run(["ln", "-s", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
 

@@ -4,17 +4,19 @@ cd /home/lbecquey/Projects/RNANet
 rm -rf latest_run.log errors.txt
 
 # Run RNANet
-bash -c 'time ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -r 20.0 -s --archive' &> latest_run.log
+bash -c 'time ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -r 20.0 --extract -s --archive' > latest_run.log 2>&1
+echo 'Compressing RNANet.db.gz...' >> latest_run.log
 touch results/RNANet.db                                         # update last modification date
 gzip -k /home/lbecquey/Projects/RNANet/results/RNANet.db        # compress it
 rm -f results/RNANet.db-wal results/RNANet.db-shm               # SQLite temporary files
 
 # Save the latest results
-export DATE=`printf '%(%Y%m%d)T'`
+export DATE=`date +%Y%m%d`
+echo "Creating new release in ./archive/ folder ($DATE)..." >> latest_run.log
 cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_latest.csv
-cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_$DATE.csv
+cp /home/lbecquey/Projects/RNANet/results/summary.csv "/home/lbecquey/Projects/RNANet/archive/summary_$DATE.csv"
 cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_latest.csv
-cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_$DATE.csv
+cp /home/lbecquey/Projects/RNANet/results/families.csv "/home/lbecquey/Projects/RNANet/archive/families_$DATE.csv"
 cp /home/lbecquey/Projects/RNANet/results/frequencies.csv /home/lbecquey/Projects/RNANet/archive/frequencies_latest.csv
 cp /home/lbecquey/Projects/RNANet/results/pair_types.csv /home/lbecquey/Projects/RNANet/archive/pair_types_latest.csv
 mv /home/lbecquey/Projects/RNANet/results/RNANet.db.gz /home/lbecquey/Projects/RNANet/archive/