Mercurial > repos > iuc > data_manager_build_bracken_database

annotate data_manager/bracken_build_database.py @ 6:84cc0dc92b0c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit c0f150357d52e21443197b2ec1427feb9fc7971e
author iuc
date Wed, 06 Mar 2024 14:09:08 +0000
parents 3c7d2c84cb09
children
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c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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1 #!/usr/bin/env python
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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3 from __future__ import print_function
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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5 import argparse
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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6 import errno
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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7 import json
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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8 import os
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9 import subprocess
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10 import uuid
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c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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13 DATA_TABLE_NAME = "bracken_databases"
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c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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16 def bracken_build_database(target_directory, bracken_build_args, database_name, prebuilt=False, data_table_name=DATA_TABLE_NAME):
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18 database_value = str(uuid.uuid4())
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20 database_name = database_name
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22 database_path = os.path.join(bracken_build_args['kraken_database'], 'database' + str(bracken_build_args['read_len']) + 'mers.kmer_distrib')
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24 if not prebuilt:
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25 bracken_build_args_list = [
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26 '-t', bracken_build_args['threads'],
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27 '-k', bracken_build_args['kmer_len'],
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28 '-l', bracken_build_args['read_len'],
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29 '-d', bracken_build_args['kraken_database'],
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30 ]
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32 subprocess.check_call(['bracken-build'] + bracken_build_args_list)
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34 data_table_entry = {
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35 "data_tables": {
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36 data_table_name: [
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37 {
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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38 "value": database_value,
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39 "name": database_name,
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40 "path": database_path,
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41 }
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42 ]
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43 }
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44 }
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46 return data_table_entry
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49 def main():
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50 parser = argparse.ArgumentParser()
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51 parser.add_argument('data_manager_json')
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52 parser.add_argument('--threads', dest='threads', default=1, help='threads')
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53 parser.add_argument('--kmer-len', dest='kmer_len', help='K-mer length')
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54 parser.add_argument('--read-len', dest='read_len', help='Read length')
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55 parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database')
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56 parser.add_argument('--database-name', dest='database_name', help='Database Name')
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57 parser.add_argument('--prebuilt', action='store_true', dest='prebuilt', help='Use pre-built DB')
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58 args = parser.parse_args()
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60 with open(args.data_manager_json) as fh:
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61 data_manager_input = json.load(fh)
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63 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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64
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65 if args.prebuilt:
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66 bracken_build_args = {
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67 'threads': args.threads,
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68 'read_len': args.read_len,
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69 'kraken_database': args.kraken_database,
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70 }
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71 else:
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72 bracken_build_args = {
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73 'threads': args.threads,
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74 'kmer_len': args.kmer_len,
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75 'read_len': args.read_len,
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76 'kraken_database': args.kraken_database,
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77 }
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78
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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79 try:
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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80 os.mkdir(target_directory)
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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81 except OSError as exc:
2
fd5830f88314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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82 if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
0
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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83 pass
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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84 else:
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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85 raise
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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86
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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87 data_manager_output = {}
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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88
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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89 data_manager_output = bracken_build_database(
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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90 target_directory,
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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91 bracken_build_args,
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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92 args.database_name,
3
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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93 args.prebuilt,
0
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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94 )
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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95
2
fd5830f88314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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96 with open(args.data_manager_json, 'w') as fh:
fd5830f88314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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97 json.dump(data_manager_output, fh, sort_keys=True)
0
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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98
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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99
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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100 if __name__ == "__main__":
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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101 main()