Louis BECQUEY / RNANet

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Louis BECQUEY
836c5a6b 1 parent c2b79e33

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Showing 4 changed files with 12 additions and 7 deletions
...@@ -1200,11 +1200,13 @@ class Pipeline: ...@@ -1200,11 +1200,13 @@ class Pipeline:
1200 # Check for a list of known problems: 1200 # Check for a list of known problems:
1201 if os.path.isfile(runDir + "/known_issues.txt"): 1201 if os.path.isfile(runDir + "/known_issues.txt"):
1202 with open(runDir + "/known_issues.txt", 'r') as issues: 1202 with open(runDir + "/known_issues.txt", 'r') as issues:
1203 - self.known_issues = [x[:-1] for x in issues.readlines()] 1203 + if self.HOMOLOGY:
1204 + self.known_issues = [ x[:-1] for x in issues.readlines() if '-' in x ]
1205 + else:
1206 + self.known_issues = [ x[:-1] for x in issues.readlines() id not '-' in x ]
1204 if self.USE_KNOWN_ISSUES: 1207 if self.USE_KNOWN_ISSUES:
1205 print("\t> Ignoring known issues:") 1208 print("\t> Ignoring known issues:")
1206 - for x in self.known_issues: 1209 + print(" ".join(self.known_issues")
1207 - print("\t ", x)
1208 1210
1209 if self.HOMOLOGY: 1211 if self.HOMOLOGY:
1210 # Ask Rfam if some are mapped to Rfam families 1212 # Ask Rfam if some are mapped to Rfam families
...@@ -1560,6 +1562,7 @@ class Pipeline: ...@@ -1560,6 +1562,7 @@ class Pipeline:
1560 if self.ARCHIVE: 1562 if self.ARCHIVE:
1561 os.makedirs(runDir + "/archive", exist_ok=True) 1563 os.makedirs(runDir + "/archive", exist_ok=True)
1562 datestr = time.strftime('%Y%m%d') 1564 datestr = time.strftime('%Y%m%d')
1565 + subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
1563 subprocess.run(["tar", "-C", path_to_3D_data + "/datapoints", "-czf", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", "."]) 1566 subprocess.run(["tar", "-C", path_to_3D_data + "/datapoints", "-czf", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", "."])
1564 subprocess.run(["ln", "-s", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"]) 1567 subprocess.run(["ln", "-s", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
1565 1568
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...@@ -4,17 +4,19 @@ cd /home/lbecquey/Projects/RNANet ...@@ -4,17 +4,19 @@ cd /home/lbecquey/Projects/RNANet
4 rm -rf latest_run.log errors.txt 4 rm -rf latest_run.log errors.txt
5 5
6 # Run RNANet 6 # Run RNANet
7 -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 7 +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
8 +echo 'Compressing RNANet.db.gz...' >> latest_run.log
8 touch results/RNANet.db # update last modification date 9 touch results/RNANet.db # update last modification date
9 gzip -k /home/lbecquey/Projects/RNANet/results/RNANet.db # compress it 10 gzip -k /home/lbecquey/Projects/RNANet/results/RNANet.db # compress it
10 rm -f results/RNANet.db-wal results/RNANet.db-shm # SQLite temporary files 11 rm -f results/RNANet.db-wal results/RNANet.db-shm # SQLite temporary files
11 12
12 # Save the latest results 13 # Save the latest results
13 -export DATE=`printf '%(%Y%m%d)T'` 14 +export DATE=`date +%Y%m%d`
15 +echo "Creating new release in ./archive/ folder ($DATE)..." >> latest_run.log
14 cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_latest.csv 16 cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_latest.csv
15 -cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_$DATE.csv 17 +cp /home/lbecquey/Projects/RNANet/results/summary.csv "/home/lbecquey/Projects/RNANet/archive/summary_$DATE.csv"
16 cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_latest.csv 18 cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_latest.csv
17 -cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_$DATE.csv 19 +cp /home/lbecquey/Projects/RNANet/results/families.csv "/home/lbecquey/Projects/RNANet/archive/families_$DATE.csv"
18 cp /home/lbecquey/Projects/RNANet/results/frequencies.csv /home/lbecquey/Projects/RNANet/archive/frequencies_latest.csv 20 cp /home/lbecquey/Projects/RNANet/results/frequencies.csv /home/lbecquey/Projects/RNANet/archive/frequencies_latest.csv
19 cp /home/lbecquey/Projects/RNANet/results/pair_types.csv /home/lbecquey/Projects/RNANet/archive/pair_types_latest.csv 21 cp /home/lbecquey/Projects/RNANet/results/pair_types.csv /home/lbecquey/Projects/RNANet/archive/pair_types_latest.csv
20 mv /home/lbecquey/Projects/RNANet/results/RNANet.db.gz /home/lbecquey/Projects/RNANet/archive/ 22 mv /home/lbecquey/Projects/RNANet/results/RNANet.db.gz /home/lbecquey/Projects/RNANet/archive/
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