Mercurial > repos > iuc > data_manager_gemini_database_downloader

annotate data_manager/data_manager_gemini_download.py @ 8:52b6a4d98009 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:49:35 +0000
parents 5bcf0e24f42c
children 27a6a256cd23
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1 #!/usr/bin/env python
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2
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3 import datetime
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4 import json
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172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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5 import os
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6 import subprocess
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7 import sys
172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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9 import yaml
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12 def write_gemini_config(config, config_file):
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13 with open(config_file, 'w') as fo:
b4b2b284230a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 9981ac1338c91a3ab46557ce6b821da3d5b4bc86
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14 yaml.dump(config, fo, allow_unicode=False, default_flow_style=False)
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17 def main():
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18 today = datetime.date.today()
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52b6a4d98009 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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19 with open(sys.argv[1]) as fh:
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20 params = json.load(fh)
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5bcf0e24f42c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 73ea765822334d9afc2f7b2ef4ddfc1a3fd4289e"
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21 target_directory = params['output_data'][0]['extra_files_path']
5bcf0e24f42c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 73ea765822334d9afc2f7b2ef4ddfc1a3fd4289e"
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22 os.mkdir(target_directory)
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24 # Generate a minimal configuration file for GEMINI update
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25 # to instruct the tool to download the annotation data into a
b4b2b284230a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 9981ac1338c91a3ab46557ce6b821da3d5b4bc86
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26 # subfolder of the target directory.
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27 config_file = os.path.join(target_directory, 'gemini-config.yaml')
b4b2b284230a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 9981ac1338c91a3ab46557ce6b821da3d5b4bc86
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28 anno_dir = os.path.join(target_directory, 'gemini/data')
b4b2b284230a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 9981ac1338c91a3ab46557ce6b821da3d5b4bc86
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29 gemini_bootstrap_config = {'annotation_dir': anno_dir}
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30 write_gemini_config(gemini_bootstrap_config, config_file)
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32 # Now gemini update can be called to download the data.
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33 # The GEMINI_CONFIG environment variable lets the tool discover
b4b2b284230a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 9981ac1338c91a3ab46557ce6b821da3d5b4bc86
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34 # the configuration file we prepared for it.
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35 # Note that the tool will rewrite the file turning it into a
b4b2b284230a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 9981ac1338c91a3ab46557ce6b821da3d5b4bc86
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36 # complete gemini configuration file.
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37 gemini_env = os.environ.copy()
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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38 gemini_env['GEMINI_CONFIG'] = target_directory
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39 cmd = "gemini update --dataonly %s %s" % (
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40 params['param_dict']['gerp_bp'],
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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41 params['param_dict']['cadd']
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42 )
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5bcf0e24f42c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 73ea765822334d9afc2f7b2ef4ddfc1a3fd4289e"
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43 subprocess.check_call(cmd, shell=True, env=gemini_env)
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45 # GEMINI tool wrappers that need access to the annotation files
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46 # are supposed to symlink them into a gemini/data subfolder of
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47 # the job working directory. To have GEMINI discover them there,
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48 # we need to set this location as the 'annotation_dir' in the
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49 # configuration file.
4
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50 with open(config_file) as fi:
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51 config = yaml.load(fi)
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52 config['annotation_dir'] = 'gemini/data'
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53 write_gemini_config(config, config_file)
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54
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55 # The name of the database should reflect whether it was built with or
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56 # without the optional GERP-bp data, the CADD scores, or both.
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57 # This builds up the correpsonding part of the name:
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58 anno_extras = []
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59 if params['param_dict']['gerp_bp']:
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60 anno_extras.append('GERP')
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61 if params['param_dict']['cadd']:
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62 anno_extras.append('CADD')
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63 if anno_extras:
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64 anno_desc = ' w/ ' + ' & '.join(anno_extras)
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65 else:
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66 anno_desc = ''
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67
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68 # Finally, we prepare the metadata for the new data table record ...
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69 data_manager_dict = {
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70 'data_tables': {
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71 'gemini_versioned_databases': [
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72 {
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73 'value': today.isoformat(),
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74 'dbkey': 'hg19',
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75 'version': params['param_dict']['gemini_db_version'],
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76 'name':
6
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77 'GEMINI annotations%s (%s snapshot)' % (
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78 anno_desc, today.isoformat()
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79 ),
4
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80 'path': './%s' % today.isoformat()
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81 }
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82 ]
172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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83 }
172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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84 }
0
fd9e9ac5ecb3 Imported from capsule None
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85
5
b4b2b284230a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 9981ac1338c91a3ab46557ce6b821da3d5b4bc86
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86 # ... and save it to the json results file
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52b6a4d98009 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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87 with open(sys.argv[1], 'w') as fh:
52b6a4d98009 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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88 json.dump(data_manager_dict, fh, sort_keys=True)
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89
3
172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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90
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91 if __name__ == "__main__":
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92 main()