Louis BECQUEY / RNANet

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Louis BECQUEY
bd665f4f 1 parent 18394e1c

Nt-specific Biopython PortionSelector

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Showing 4 changed files with 8 additions and 6 deletions
...@@ -3,7 +3,8 @@ nohup.out ...@@ -3,7 +3,8 @@ nohup.out
3 log_of_the_run.sh 3 log_of_the_run.sh
4 4
5 # results 5 # results
6 -results/ 6 +results/*
7 +logs/*
7 8
8 # temporary results files 9 # temporary results files
9 data/ 10 data/
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...@@ -3,7 +3,7 @@ ...@@ -3,7 +3,7 @@
3 # Run RNANet 3 # Run RNANet
4 cd /home/lbecquey/Projects/RNANet; 4 cd /home/lbecquey/Projects/RNANet;
5 rm -f stdout.txt stderr.txt errors.txt; 5 rm -f stdout.txt stderr.txt errors.txt;
6 -time './RNAnet.py --3d-folder /home/lbequey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/' > stdout.txt 2> stderr.txt; 6 +time './RNAnet.py --3d-folder /home/lbequey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -s -r 20.0' > stdout.txt 2> stderr.txt;
7 7
8 # Sync in Seafile 8 # Sync in Seafile
9 seaf-cli start; 9 seaf-cli start;
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...@@ -433,6 +433,7 @@ def to_dist_matrix(f): ...@@ -433,6 +433,7 @@ def to_dist_matrix(f):
433 notify(f"Computed {f} distance matrix", "loaded from file") 433 notify(f"Computed {f} distance matrix", "loaded from file")
434 return 0 434 return 0
435 435
436 + notify(f"Computing {f} distance matrix from alignment...")
436 dm = DistanceCalculator('identity') 437 dm = DistanceCalculator('identity')
437 with open(path_to_seq_data+"/realigned/"+f+"++.afa") as al_file: 438 with open(path_to_seq_data+"/realigned/"+f+"++.afa") as al_file:
438 al = AlignIO.read(al_file, "fasta")[-len(mappings_list[f]):] 439 al = AlignIO.read(al_file, "fasta")[-len(mappings_list[f]):]
...@@ -542,10 +543,10 @@ if __name__ == "__main__": ...@@ -542,10 +543,10 @@ if __name__ == "__main__":
542 threads = [ 543 threads = [
543 th.Thread(target=reproduce_wadley_results, kwargs={'carbon': 1}), 544 th.Thread(target=reproduce_wadley_results, kwargs={'carbon': 1}),
544 th.Thread(target=reproduce_wadley_results, kwargs={'carbon': 4}), 545 th.Thread(target=reproduce_wadley_results, kwargs={'carbon': 4}),
545 - # th.Thread(target=stats_len), # computes figures 546 + th.Thread(target=stats_len), # computes figures
546 - # th.Thread(target=stats_freq), # Updates the database 547 + th.Thread(target=stats_freq), # Updates the database
547 - # th.Thread(target=seq_idty), # produces .npy files and seq idty figures 548 + th.Thread(target=seq_idty), # produces .npy files and seq idty figures
548 - # th.Thread(target=per_chain_stats) # Updates the database 549 + th.Thread(target=per_chain_stats) # Updates the database
549 ] 550 ]
550 551
551 # Start the threads 552 # Start the threads
......