Mercurial > repos > iuc > data_manager_snpeff
annotate data_manager/data_manager_snpEff_databases.py @ 7:a6400027d849 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
author | iuc |
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date | Tue, 24 Oct 2017 07:27:38 -0400 |
parents | 2107b4f40945 |
children | 08d7998c3afb |
rev | line source |
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0 | 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
iuc
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0
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changeset
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3 import optparse |
0 | 4 import os |
5 import subprocess | |
1
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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changeset
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6 import sys |
0 | 7 |
8 | |
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3d9dd4b9fb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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9 def fetch_databases(data_manager_dict, target_directory): |
0 | 10 if not os.path.exists(target_directory): |
11 os.makedirs(target_directory) | |
12 databases_path = os.path.join( target_directory, 'databases.out' ) | |
1
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
diff
changeset
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13 databases_output = open(databases_path, 'w') |
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3d9dd4b9fb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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4
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14 args = ['snpEff', 'databases'] |
3d9dd4b9fb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents:
4
diff
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15 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno()) |
0 | 16 if return_code: |
17 sys.exit( return_code ) | |
18 databases_output.close() | |
1
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
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changeset
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19 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) |
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2107b4f40945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit e32db0704e23d58358f749177988d2cb5f01c708
iuc
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5
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20 data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get( 'snpeffv_databases', [] ) |
1
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
diff
changeset
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21 data_table_entries = [] |
5
3d9dd4b9fb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents:
4
diff
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22 with open(databases_path, 'r') as fh: |
1
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
diff
changeset
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23 for i, line in enumerate(fh): |
0 | 24 fields = line.split('\t') |
25 if len(fields) >= 2: | |
26 genome_version = fields[0].strip() | |
27 if genome_version.startswith("Genome") or genome_version.startswith("-"): | |
28 continue | |
1
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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0
diff
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29 # snpeff test genome |
0 | 30 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): |
31 continue | |
32 description = fields[1].strip() + ' : ' + genome_version | |
33 data_table_entries.append(dict(value=genome_version, name=description)) | |
6
2107b4f40945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit e32db0704e23d58358f749177988d2cb5f01c708
iuc
parents:
5
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34 data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries |
0 | 35 return data_manager_dict |
36 | |
1
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
diff
changeset
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37 |
0 | 38 def main(): |
39 parser = optparse.OptionParser() | |
40 (options, args) = parser.parse_args() | |
41 | |
42 filename = args[0] | |
43 | |
1
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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0
diff
changeset
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44 params = json.loads( open( filename ).read() ) |
0 | 45 target_directory = params[ 'output_data' ][0]['extra_files_path'] |
46 os.mkdir( target_directory ) | |
47 data_manager_dict = {} | |
48 | |
1
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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0
diff
changeset
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49 # Create Defuse Reference Data |
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3d9dd4b9fb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents:
4
diff
changeset
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50 data_manager_dict = fetch_databases( data_manager_dict, target_directory) |
0 | 51 |
1
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
diff
changeset
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52 # save info to json file |
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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0
diff
changeset
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53 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) |
0 | 54 |
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847b0f43c0e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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1
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changeset
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55 |
1
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
diff
changeset
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56 if __name__ == "__main__": |
85a23e2dd92b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
0
diff
changeset
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57 main() |