Mercurial > repos > devteam > data_manager_picard_index_builder
annotate data_manager/picard_index_builder.py @ 4:99847f7b3a32 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 59ee07d9786f1a090053b4a13192247872389d61
author | iuc |
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date | Mon, 10 Apr 2017 06:06:09 -0400 |
parents | 0663d25e619c |
children | acaa6719a478 |
rev | line source |
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0 | 1 #!/usr/bin/env python |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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2 # Dan Blankenberg |
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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3 from __future__ import print_function |
0 | 4 |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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5 import optparse |
0 | 6 import os |
7 import subprocess | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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changeset
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8 import sys |
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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9 from json import dumps, loads |
0 | 10 |
11 DEFAULT_DATA_TABLE_NAME = "picard_indexes" | |
12 | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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13 |
0 | 14 def get_id_name( params, dbkey, fasta_description=None): |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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15 # TODO: ensure sequence_id is unique and does not already appear in location file |
0 | 16 sequence_id = params['param_dict']['sequence_id'] |
17 if not sequence_id: | |
18 sequence_id = dbkey | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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19 |
0 | 20 sequence_name = params['param_dict']['sequence_name'] |
21 if not sequence_name: | |
22 sequence_name = fasta_description | |
23 if not sequence_name: | |
24 sequence_name = dbkey | |
25 return sequence_id, sequence_name | |
26 | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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27 |
0 | 28 def build_picard_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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changeset
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29 # TODO: allow multiple FASTA input files |
0 | 30 fasta_base_name = os.path.split( fasta_filename )[-1] |
31 prefix = os.path.splitext( fasta_base_name )[0] | |
32 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) | |
33 os.symlink( fasta_filename, sym_linked_fasta_filename ) | |
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99847f7b3a32
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 59ee07d9786f1a090053b4a13192247872389d61
iuc
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34 args = [ 'picard', 'CreateSequenceDictionary', 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix ] |
0 | 35 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) |
36 return_code = proc.wait() | |
37 if return_code: | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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38 print("Error building index.", file=sys.stderr) |
0 | 39 sys.exit( return_code ) |
40 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) | |
41 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) | |
42 | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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43 |
0 | 44 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): |
45 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
46 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) | |
47 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) | |
48 return data_manager_dict | |
49 | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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50 |
0 | 51 def main(): |
52 parser = optparse.OptionParser() | |
53 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) | |
54 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) | |
55 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) | |
56 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) | |
57 (options, args) = parser.parse_args() | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
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changeset
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58 |
0 | 59 filename = args[0] |
3
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
diff
changeset
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60 |
0 | 61 params = loads( open( filename ).read() ) |
62 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
63 os.mkdir( target_directory ) | |
64 data_manager_dict = {} | |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
0
diff
changeset
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65 |
0 | 66 dbkey = options.fasta_dbkey |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
diff
changeset
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67 |
0 | 68 if dbkey in [ None, '', '?' ]: |
69 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) | |
3
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
diff
changeset
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70 |
0 | 71 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
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72 |
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
diff
changeset
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73 # build the index |
0 | 74 build_picard_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
diff
changeset
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75 |
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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0
diff
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76 # save info to json file |
0 | 77 open( filename, 'wb' ).write( dumps( data_manager_dict ) ) |
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0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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78 |
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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79 |
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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80 if __name__ == "__main__": |
0663d25e619c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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81 main() |