Mercurial > repos > sanbi-uwc > data_manager_shapeit2_reference

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planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
author sanbi-uwc
date Tue, 18 Sep 2018 00:54:49 -0400
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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diff changeset
1 #!/usr/bin/env python3
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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3 from __future__ import division, print_function
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4 import argparse
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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5 import json
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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6 import os
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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7 import os.path
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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10 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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11 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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12 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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13 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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14 return data_manager_dict
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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17 _add_data_table_entry.__annotations__ = {'data_manager': dict, 'data_table_name': str, 'data_table_entry': dict, 'return': dict}
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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20 def assert_prefix_exists(prefix, path, prefix_type):
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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21 prefix_exists = False
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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22 for filename in os.listdir(path):
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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23 if filename.startswith(prefix):
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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24 prefix_exists = True
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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25 break
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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26 else:
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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27 if not prefix_exists:
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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28 exit("Unable to find a file with {} prefix {} in {}".format(prefix_type, prefix, path))
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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31 assert_prefix_exists.__annotations__ = {'prefix': str, 'path': str, 'prefix_type': str, 'return': None}
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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33 if __name__ == '__main__':
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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34 parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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35 parser.add_argument('key', help='Short key to identify this reference set (no spaces)')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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36 parser.add_argument('name', help='Description of reference set')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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37 parser.add_argument('path', help='Filesystem path to directory containing this reference set')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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38 parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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39 parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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40 parser.add_argument('sample_prefix', help='Filename prefix for sample file in this reference set')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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41 parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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42 args = parser.parse_args()
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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44 if not os.path.exists(args.path):
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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45 exit("Unable to find specified path {}".format(args.path))
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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47 assert_prefix_exists(args.reference_prefix, args.path, 'reference')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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48 assert_prefix_exists(args.map_prefix, args.path, 'map')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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49 assert_prefix_exists(args.sample_prefix, args.path, 'sample')
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
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sanbi-uwc
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51 for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix', 'sample_prefix'):
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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52 value = getattr(args, column)
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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53 if '\t' in value:
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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54 exit("TAB character found in {} argument".format(column))
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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56 data_manager_dict = {}
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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57 data_table_entry = dict(value=args.key, name=args.name, path=args.path,
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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58 reference_prefix=args.reference_prefix, map_prefix=args.map_prefix,
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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59 sample_prefix=args.sample_prefix)
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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60 _add_data_table_entry(data_manager_dict, 'shapeit2_ref', data_table_entry)
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
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4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
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62 args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')