Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_databases.py @ 11:def511e8e005 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
author iuc
date Tue, 24 Nov 2020 07:27:28 +0000 (2020-11-24)
parents c6fbc5421697
children
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1 #!/usr/bin/env python
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85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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2 import json
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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3 import optparse
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4 import os
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5 import subprocess
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6 import sys
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8
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9 def fetch_databases(data_manager_dict, target_directory):
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10 if not os.path.exists(target_directory):
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11 os.makedirs(target_directory)
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12 databases_path = os.path.join(target_directory, 'databases.out')
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13 args = ['snpEff', 'databases']
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14 with open(databases_path, 'w') as databases_output:
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15 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
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16 if return_code:
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17 sys.exit(return_code)
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18 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
08d7998c3afb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
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19 data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', [])
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20 data_table_entries = []
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21 with open(databases_path, 'r') as fh:
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22 for line in fh:
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23 fields = line.split('\t')
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24 if len(fields) >= 2:
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25 genome_version = fields[0].strip()
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26 if genome_version.startswith("Genome") or genome_version.startswith("-"):
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27 continue
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28 # snpeff test genome
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29 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
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30 continue
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31 description = fields[1].strip() + ' : ' + genome_version
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32 data_table_entries.append(dict(value=genome_version, name=description))
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33 data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
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34 return data_manager_dict
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37 def main():
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38 parser = optparse.OptionParser()
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39 (options, args) = parser.parse_args()
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41 filename = args[0]
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42
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43 with open(filename) as fh:
c6fbc5421697 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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44 params = json.load(fh)
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45 target_directory = params['output_data'][0]['extra_files_path']
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46 os.mkdir(target_directory)
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47 data_manager_dict = {}
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49 # Create Defuse Reference Data
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50 data_manager_dict = fetch_databases(data_manager_dict, target_directory)
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52 # save info to json file
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53 with open(filename, 'w') as fh:
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54 json.dump(data_manager_dict, fh, sort_keys=True)
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57 if __name__ == "__main__":
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58 main()