Mercurial > repos > iuc > data_manager_hisat2_index_builder

annotate data_manager/hisat2_index_builder.py @ 6:f2ff73198a63 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:27:15 +0000
parents 721a2a97f31b
children
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iuc
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1 #!/usr/bin/env python
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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2 # Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
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3 from __future__ import print_function
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5 import argparse
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f2ff73198a63 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
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6 import json
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7 import os
a9a26db6a455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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8 import shlex
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9 import subprocess
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10 import sys
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12 DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"
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15 def get_id_name(params, dbkey, fasta_description=None):
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16 # TODO: ensure sequence_id is unique and does not already appear in location file
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17 sequence_id = params['param_dict']['sequence_id']
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18 if not sequence_id:
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19 sequence_id = dbkey
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21 sequence_name = params['param_dict']['sequence_name']
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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22 if not sequence_name:
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23 sequence_name = fasta_description
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24 if not sequence_name:
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25 sequence_name = dbkey
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26 return sequence_id, sequence_name
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29 def build_hisat_index(data_manager_dict, options, params, sequence_id, sequence_name):
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8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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30 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
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31 target_directory = params['output_data'][0]['extra_files_path']
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32 if not os.path.exists(target_directory):
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33 os.mkdir(target_directory)
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34 fasta_base_name = os.path.split(options.fasta_filename)[-1]
721a2a97f31b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
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35 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
721a2a97f31b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
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36 os.symlink(options.fasta_filename, sym_linked_fasta_filename)
721a2a97f31b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
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37 args = ['hisat2-build']
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38 args.extend(shlex.split(options.indexer_options))
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39 args.extend([sym_linked_fasta_filename, sequence_id])
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40 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
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41 return_code = proc.wait()
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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42 if return_code:
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43 print("Error building index.", file=sys.stderr)
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44 sys.exit(return_code)
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45 data_table_entry = dict(value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id)
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46 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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48
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49 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
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50 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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51 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
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52 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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53 return data_manager_dict
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56 def main():
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57 # Parse Command Line
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58 parser = argparse.ArgumentParser()
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59 parser.add_argument('--output', dest='output', action='store', type=str, default=None)
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60 parser.add_argument('--fasta_filename', dest='fasta_filename', action='store', type=str, default=None)
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61 parser.add_argument('--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None)
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62 parser.add_argument('--fasta_description', dest='fasta_description', action='store', type=str, default=None)
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63 parser.add_argument('--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes')
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64 parser.add_argument('--indexer_options', dest='indexer_options', action='store', type=str, default='')
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65 options = parser.parse_args()
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67 filename = options.output
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69 with open(filename) as fh:
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70 params = json.load(fh)
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71 data_manager_dict = {}
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73 if options.fasta_dbkey in [None, '', '?']:
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74 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (options.fasta_dbkey))
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721a2a97f31b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
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76 sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)
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8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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77
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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78 # build the index
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721a2a97f31b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
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79 build_hisat_index(data_manager_dict, options, params, sequence_id, sequence_name)
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8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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80
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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81 # save info to json file
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f2ff73198a63 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
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82 with open(filename, 'w') as fh:
f2ff73198a63 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
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83 json.dump(data_manager_dict, fh, sort_keys=True)
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a9a26db6a455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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84
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8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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85
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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86 if __name__ == "__main__":
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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87 main()