Mercurial > repos > devteam > data_manager_bowtie2_index_builder
changeset 8:1586b111d2a3 draft
"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 12:44:43 +0000 |
| parents | 1c0f8e9d87c6 |
| children | 76672b83d42d |
| files | data_manager/bowtie2_index_builder.py |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/data_manager/bowtie2_index_builder.py Mon Apr 06 19:27:05 2020 -0400 +++ b/data_manager/bowtie2_index_builder.py Sun Nov 22 12:44:43 2020 +0000 @@ -2,11 +2,11 @@ # Dan Blankenberg from __future__ import print_function +import json import optparse import os import subprocess import sys -from json import dumps, loads DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"] @@ -61,7 +61,8 @@ filename = args[0] - params = loads(open(filename).read()) + with open(filename) as fh: + params = json.load(fh) target_directory = params['output_data'][0]['extra_files_path'] os.mkdir(target_directory) data_manager_dict = {} @@ -77,8 +78,8 @@ 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) # save info to json file - with open(filename, 'w') as json_out: - json_out.write(dumps(data_manager_dict, sort_keys=True)) + with open(filename, 'w') as fh: + json.dump(data_manager_dict, fh, sort_keys=True) if __name__ == "__main__":