Mercurial > repos > devteam > data_manager_bowtie2_index_builder

comparison data_manager/bowtie2_index_builder.py @ 10:e816eef8a48f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:39:27 +0000
parents 47432d88b0a0
children
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9:47432d88b0a0 10:e816eef8a48f
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 # Dan Blankenberg 2 # Dan Blankenberg
3 from __future__ import print_function 3 from __future__ import print_function
4 4
5 import json
5 import optparse 6 import optparse
6 import os 7 import os
7 import subprocess 8 import subprocess
8 import sys 9 import sys
9 from json import dumps, loads
10 10
11 DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"] 11 DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"]
12 12
13 13
14 def get_id_name(params, dbkey, fasta_description=None): 14 def get_id_name(params, dbkey, fasta_description=None):
59 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name') 59 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name')
60 (options, args) = parser.parse_args() 60 (options, args) = parser.parse_args()
61 61
62 filename = args[0] 62 filename = args[0]
63 63
64 params = loads(open(filename).read()) 64 with open(filename) as fh:
65 params = json.load(fh)
65 target_directory = params['output_data'][0]['extra_files_path'] 66 target_directory = params['output_data'][0]['extra_files_path']
66 os.mkdir(target_directory) 67 os.mkdir(target_directory)
67 data_manager_dict = {} 68 data_manager_dict = {}
68 69
69 dbkey = options.fasta_dbkey 70 dbkey = options.fasta_dbkey
75 76
76 # build the index 77 # build the index
77 build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES) 78 build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)
78 79
79 # save info to json file 80 # save info to json file
80 with open(filename, 'w') as json_out: 81 with open(filename, 'w') as fh:
81 json_out.write(dumps(data_manager_dict, sort_keys=True)) 82 json.dump(data_manager_dict, fh, sort_keys=True)
82 83
83 84
84 if __name__ == "__main__": 85 if __name__ == "__main__":
85 main() 86 main()