Mercurial > repos > iuc > data_manager_build_kma_index

annotate data_manager/kma_build_index.py @ 2:2c532a6eee3f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:45:39 +0000
parents 8c2e674a93bb
children
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889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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1 #!/usr/bin/env python
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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3 from __future__ import print_function
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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5 import argparse
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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6 import errno
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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7 import json
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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8 import os
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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9 import subprocess
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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10 import uuid
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889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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13 DATA_TABLE_NAME = "kma_index"
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889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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16 def kma_build_index(kma_index_args, index_name, target_directory, data_table_name=DATA_TABLE_NAME):
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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17 UUID = str(uuid.uuid4())
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19 os.mkdir(os.path.join(target_directory, UUID))
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889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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21 args = [
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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22 '-k', str(kma_index_args["k"]),
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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23 '-k_t', str(kma_index_args["k_t"]),
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24 '-k_i', str(kma_index_args["k_i"]),
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25 '-ML', str(kma_index_args["ML"]),
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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26 '-ht', str(kma_index_args["ht"]),
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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27 '-hq', str(kma_index_args["hq"]),
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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28 '-o', os.path.join(UUID, "index"),
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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29 '-i', " ".join(kma_index_args["fasta"]),
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30 ]
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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32 subprocess.check_call(' '.join(['kma index'] + args), cwd=target_directory, shell=True)
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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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 {
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38 "value": UUID,
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39 "name": index_name,
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40 "path": os.path.join(UUID, "index"),
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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(args):
2
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50 with open(args.data_manager_json) as fh:
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51 data_manager_input = json.load(fh)
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53 target_directory = data_manager_input['output_data'][0]['extra_files_path']
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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54
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55 try:
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56 os.mkdir(target_directory)
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57 except OSError as exc:
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58 if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
0
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59 pass
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60 else:
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61 raise
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63 data_manager_output = {}
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64
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65 kma_index_args = {
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66 "k": args.k,
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67 "k_t": args.k_t,
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68 "k_i": args.k_i,
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69 "ML": args.ML,
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70 "ht": args.ht,
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71 "hq": args.hq,
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72 "fasta": args.fasta,
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73 }
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75 data_manager_output = kma_build_index(
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76 kma_index_args,
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77 args.index_name,
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78 target_directory,
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79 )
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80
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81 with open(args.data_manager_json, 'w') as fh:
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82 json.dump(data_manager_output, fh, sort_keys=True)
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84
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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85 if __name__ == "__main__":
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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86 parser = argparse.ArgumentParser()
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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87 parser.add_argument('data_manager_json')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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88 parser.add_argument('--k', dest='k', type=int, default=16, help='')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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89 parser.add_argument('--k_t', dest='k_t', type=int, default=16, help='')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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90 parser.add_argument('--k_i', dest='k_i', type=int, default=16, help='')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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91 parser.add_argument('--ML', dest='ML', type=int, default=16, help='')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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92 parser.add_argument('--ht', dest='ht', type=float, default=1.0, help='')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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93 parser.add_argument('--hq', dest='hq', type=float, default=1.0, help='')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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94 parser.add_argument('--name', dest='index_name', help='')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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95 parser.add_argument('fasta', nargs='+', help='fasta file(s) to index')
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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96 args = parser.parse_args()
889cc43b72d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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97 main(args)