Mercurial > repos > iuc > data_manager_homer_preparse

annotate data_manager/homer_genome_preparse.py @ 1:20fae63ba8dc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
author iuc
date Thu, 06 Apr 2023 16:16:17 +0000
parents 5d2e5fddec81
children
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5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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1 #!/usr/bin/env python
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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2 # Dan Blankenberg for bowtie2
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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3 # Modified by Lucille Delisle for homer
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4 from __future__ import print_function
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5
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6 import json
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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7 import optparse
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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8 import os
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9 import subprocess
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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10 import sys
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12 DEFAULT_DATA_TABLE_NAME = "homer_preparse"
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5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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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
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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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']
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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22 if not sequence_name:
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23 sequence_name = fasta_description
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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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 homer_preparse(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id,
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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30 sequence_name, size, mask, version,
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31 data_table_name=DEFAULT_DATA_TABLE_NAME):
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32 args = ['preparseGenome.pl', fasta_filename, '-size', str(size), '-preparsedDir', target_directory]
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33 if mask:
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34 args.append('-mask')
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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35 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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36 return_code = proc.wait()
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37 if return_code:
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38 print("Error preparsing genome.", file=sys.stderr)
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39 sys.exit(return_code)
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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40 mask_suffix = 'r' if mask else ''
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41 mask_suffix_name = ' masked' if mask else ''
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42 data_table_entry = dict(value=sequence_id + mask_suffix + '_' + str(size), dbkey=dbkey,
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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43 mask=str(mask), size=str(size), name=sequence_name + mask_suffix_name + ' (' + str(size) + 'bp)',
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44 path=sequence_id + mask_suffix + '_' + str(size),
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45 path_fasta=fasta_filename,
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46 version=version)
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47 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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48
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50 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
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51 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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52 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
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53 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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54 return data_manager_dict
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57 def main():
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58 parser = optparse.OptionParser()
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59 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
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60 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
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61 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
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62 parser.add_option('-s', '--size', dest='size', action='store', type="int", default=200, help='fragment size')
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63 parser.add_option('-m', '--mask', dest='mask', action='store_true', default=False, help='mask the lower case bases (repeats)')
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64 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
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65 parser.add_option('--index_version', dest='index_version', action='store', type="string", default=None, help='index version')
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66 (options, args) = parser.parse_args()
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68 filename = args[0]
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69
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70 with open(filename) as fh:
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71 params = json.load(fh)
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72 target_directory = params['output_data'][0]['extra_files_path']
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73 os.mkdir(target_directory)
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74 data_manager_dict = {}
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76 dbkey = options.fasta_dbkey
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77
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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78 if dbkey in [None, '', '?']:
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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79 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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80
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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81 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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82
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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83 # preparse the genome
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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84 homer_preparse(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id,
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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85 sequence_name, options.size, options.mask, options.index_version,
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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86 data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME)
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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87
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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88 # save info to json file
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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89 with open(filename, 'w') as fh:
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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90 json.dump(data_manager_dict, fh, sort_keys=True)
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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91
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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92
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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93 if __name__ == "__main__":
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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94 main()