Mercurial > repos > dfornika > data_manager_mash_sketch_builder

annotate data_manager/mash_sketch_builder.py @ 7:bb0476d21f80 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 05fb8d8428ce9bc84837bb4043018ab2135f5727-dirty"
author dfornika
date Mon, 24 Feb 2020 18:24:58 +0000
parents 516e892d2b40
children 96dbdfb1ba4d
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647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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1 #!/usr/bin/env python
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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3 import argparse
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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4 import errno
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5 import json
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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6 import os
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7 import subprocess
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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8 import sys
7
bb0476d21f80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 05fb8d8428ce9bc84837bb4043018ab2135f5727-dirty"
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9 import uuid
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12 DATA_TABLE_NAME = "mash_sketches"
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15 def mash_sketch(mash_sketch_args, sketch_name, target_directory, data_table_name=DATA_TABLE_NAME):
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16 UUID = str(uuid.uuid4())
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18 os.mkdir(os.path.join(target_directory, UUID))
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20 sketch_path = os.path.join(UUID, "sketch"),
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22 args = [
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23 '-k', str(mash_sketch_args["kmer_size"]),
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24 '-s', str(mash_sketch_args["sketch_size"]),
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25 '-o', sketch_path,
af86557c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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26 '-p', str(mash_sketch_args["threads"]),
af86557c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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27 str(mash_sketch_args["fasta"]),
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28 ]
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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30 subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory)
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33 data_table_entry = {
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34 'data_tables': {
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35 data_table_name: [
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36 {
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37 "value": UUID,
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38 "name": sketch_name,
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39 "path": sketch_path,
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40 }
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41 ]
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42 }
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43 }
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45 return data_table_entry
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48 def main():
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49 parser = argparse.ArgumentParser()
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50 parser.add_argument('data_manager_json')
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51 parser.add_argument('--kmer-size', dest='kmer_size', type=int, default=35, help='kmer length')
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52 parser.add_argument('--sketch-size', dest='sketch_size', type=int, default=31, help='minimizer length')
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53 parser.add_argument('--fasta', dest='fasta', help='Fasta file to sketch')
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54 parser.add_argument('--threads', dest='threads', default=1, help='threads')
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55 parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch')
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56 args = parser.parse_args()
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58 data_manager_input = json.loads(open(args.data_manager_json).read())
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60 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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62 try:
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63 os.mkdir( target_directory )
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64 except OSError as exc:
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65 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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66 pass
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67 else:
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68 raise
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70 data_manager_output = {}
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72 mash_sketch_args = {
1
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73 "kmer_size": args.kmer_size,
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74 "sketch_size": args.sketch_size,
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75 "fasta": args.fasta,
0
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76 "threads": args.threads,
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77 }
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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78
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af86557c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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79 data_manager_output = mash_sketch(
af86557c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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80 mash_sketch_args,
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516e892d2b40 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 05fb8d8428ce9bc84837bb4043018ab2135f5727-dirty"
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81 args.sketch_name,
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af86557c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
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82 target_directory,
af86557c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
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83 )
af86557c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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84
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647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
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85 open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True))
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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86
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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87
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
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88 if __name__ == "__main__":
647eedfd1556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
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89 main()