Mercurial > repos > iuc > vsnp_add_zero_coverage

comparison vsnp_get_snps.py @ 9:40b97055bb99 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
author iuc
date Fri, 10 Jun 2022 06:08:02 +0000
parents 18b59c38017e
children
comparison
equal deleted inserted replaced
8:18b59c38017e 9:40b97055bb99
17 import vcf 17 import vcf
18 18
19 19
20 def get_time_stamp(): 20 def get_time_stamp():
21 return datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H-%M-%S') 21 return datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H-%M-%S')
22
23
24 def set_num_cpus(num_files, processes):
25 num_cpus = len(os.sched_getaffinity(0))
26 if num_files < num_cpus and num_files < processes:
27 return num_files
28 if num_cpus < processes:
29 half_cpus = int(num_cpus / 2)
30 if num_files < half_cpus:
31 return num_files
32 return half_cpus
33 return processes
34 22
35 23
36 def setup_all_vcfs(vcf_files, vcf_dirs): 24 def setup_all_vcfs(vcf_files, vcf_dirs):
37 # Create the all_vcfs directory and link 25 # Create the all_vcfs directory and link
38 # all input vcf files into it for processing. 26 # all input vcf files into it for processing.
463 vcf_files.append(file_path) 451 vcf_files.append(file_path)
464 452
465 multiprocessing.set_start_method('spawn') 453 multiprocessing.set_start_method('spawn')
466 queue1 = multiprocessing.JoinableQueue() 454 queue1 = multiprocessing.JoinableQueue()
467 num_files = len(vcf_files) 455 num_files = len(vcf_files)
468 cpus = set_num_cpus(num_files, args.processes)
469 # Set a timeout for get()s in the queue. 456 # Set a timeout for get()s in the queue.
470 timeout = 0.05 457 timeout = 0.05
471 458
472 # Initialize the snp_finder object. 459 # Initialize the snp_finder object.
473 snp_finder = SnpFinder(num_files, args.dbkey, args.input_excel, args.all_isolates, args.ac, args.min_mq, args.quality_score_n_threshold, args.min_quality_score, args.input_vcf_dir, args.output_json_avg_mq_dir, args.output_json_snps_dir, args.output_snps_dir, args.output_summary) 460 snp_finder = SnpFinder(num_files, args.dbkey, args.input_excel, args.all_isolates, args.ac, args.min_mq, args.quality_score_n_threshold, args.min_quality_score, args.input_vcf_dir, args.output_json_avg_mq_dir, args.output_json_snps_dir, args.output_snps_dir, args.output_summary)
493 # Populate the queue for job splitting. 480 # Populate the queue for job splitting.
494 for vcf_dir in vcf_dirs: 481 for vcf_dir in vcf_dirs:
495 queue1.put(vcf_dir) 482 queue1.put(vcf_dir)
496 483
497 # Complete the get_snps task. 484 # Complete the get_snps task.
498 processes = [multiprocessing.Process(target=snp_finder.get_snps, args=(queue1, timeout, )) for _ in range(cpus)] 485 processes = [multiprocessing.Process(target=snp_finder.get_snps, args=(queue1, timeout, )) for _ in range(args.processes)]
499 for p in processes: 486 for p in processes:
500 p.start() 487 p.start()
501 for p in processes: 488 for p in processes:
502 p.join() 489 p.join()
503 queue1.join() 490 queue1.join()