changeset 8:63d5652be07a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:46:31 +0000
parents 37580590ecfb
children 9e993022c762
files data_manager/bwa_mem_index_builder.py
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/bwa_mem_index_builder.py	Wed Dec 04 16:29:26 2019 -0500
+++ b/data_manager/bwa_mem_index_builder.py	Sun Nov 22 12:46:31 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
 
 CHUNK_SIZE = 2**20
 TWO_GB = 2**30 * 2
@@ -68,7 +68,8 @@
 
     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 = {}
@@ -93,7 +94,8 @@
     )
 
     # save info to json file
-    open(filename, 'w').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__":