Mercurial > repos > iuc > data_manager_mash_sketch_builder

annotate data_manager/mash_sketch_builder.py @ 0:19cb0604e603 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 419003af9d5cdf7466b3bbc229256da4fb5852e6"
author iuc
date Wed, 26 Feb 2020 19:03:53 +0000
parents
children 57f42fad6745
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19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
iuc
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1 #!/usr/bin/env python
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
iuc
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3 import argparse
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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4 import errno
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
iuc
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5 import json
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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6 import os
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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7 import subprocess
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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8 import uuid
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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11 DATA_TABLE_NAME = "mash_sketches"
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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14 def mash_sketch(mash_sketch_args, sketch_name, target_directory, data_table_name=DATA_TABLE_NAME):
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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15 UUID = str(uuid.uuid4())
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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17 os.mkdir(os.path.join(target_directory, UUID))
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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19 sketch_path = os.path.join(target_directory, UUID, "sketch")
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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21 args = [
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22 '-k', str(mash_sketch_args["kmer_size"]),
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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23 '-s', str(mash_sketch_args["sketch_size"]),
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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24 '-w', str(mash_sketch_args["probability_threshold"]),
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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25 '-o', str(sketch_path),
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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26 '-p', str(mash_sketch_args["threads"]),
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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27 str(mash_sketch_args["fasta"]),
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28 ]
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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30 if mash_sketch_args["individual_sequences"]:
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31 args = args + ["-i"]
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33 subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory)
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35 data_table_entry = {
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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36 'data_tables': {
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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37 data_table_name: [
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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38 {
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39 "value": UUID,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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40 "name": sketch_name,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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41 "path": UUID,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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42 }
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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43 ]
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44 }
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45 }
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47 return data_table_entry
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50 def main():
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51 parser = argparse.ArgumentParser()
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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52 parser.add_argument('data_manager_json')
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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53 parser.add_argument('--kmer-size', dest='kmer_size', type=int, default=35, help='kmer length')
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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54 parser.add_argument('--sketch-size', dest='sketch_size', type=int, default=31, help='minimizer length')
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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55 parser.add_argument('--probability-threshold', dest='probability_threshold', type=float, default=0.01, help='Probability threshold for warning about low k-mer size')
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56 parser.add_argument('--individual-sequences', dest='individual_sequences', action='store_true', default=False, help='Sketch individual sequences (for multi-fasta files)')
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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57 parser.add_argument('--fasta', dest='fasta', help='Fasta file to sketch')
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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58 parser.add_argument('--threads', dest='threads', default=1, help='threads')
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59 parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch')
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60 args = parser.parse_args()
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62 data_manager_input = json.loads(open(args.data_manager_json).read())
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64 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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65
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66 try:
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67 os.mkdir( target_directory )
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68 except OSError as exc:
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69 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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70 pass
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71 else:
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72 raise
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73
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74 data_manager_output = {}
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75
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76 mash_sketch_args = {
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77 "kmer_size": args.kmer_size,
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78 "sketch_size": args.sketch_size,
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79 "probability_threshold": args.probability_threshold,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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80 "fasta": args.fasta,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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81 "individual_sequences": args.individual_sequences,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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82 "threads": args.threads,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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83 }
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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84
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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85 data_manager_output = mash_sketch(
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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86 mash_sketch_args,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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87 args.sketch_name,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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88 target_directory,
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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89 )
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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90
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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91 open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True))
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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92
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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93
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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94 if __name__ == "__main__":
19cb0604e603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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95 main()