Mercurial > repos > greg > queue_genotype_workflow

changeset 10:41477ff2ce8e draft

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Uploaded
author greg
date Wed, 26 Aug 2020 13:49:26 -0400
parents 0ed7dc418a6d
children 560dcf3f9f3d
files queue_genotype_workflow.py
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/queue_genotype_workflow.py	Wed Jan 22 08:48:41 2020 -0500
+++ b/queue_genotype_workflow.py	Wed Aug 26 13:49:26 2020 -0400
@@ -2,13 +2,13 @@
 import argparse
 import os
 import shutil
-import string
 import sys
 import threading
 import time
+from datetime import datetime
 
 from bioblend import galaxy
-from datetime import datetime
+
 from six.moves import configparser
 
 parser = argparse.ArgumentParser()
@@ -80,7 +80,7 @@
     config_parser.read(config_file)
     for key, value in config_parser.items(section):
         if section == 'defaults':
-            d[string.upper(key)] = value
+            d[key.upper()] = value
         else:
             d[key] = value
     return d
@@ -266,7 +266,7 @@
             # Reset the default value 'no' of output_nj_phylogeny_tree to 'yes'.
             if parameter_updates is None:
                 parameter_updates = {}
-            output_nj_phylogeny_tree_dict = {'output_nj_phylogeny_tree' : 'yes'}
+            output_nj_phylogeny_tree_dict = {'output_nj_phylogeny_tree': 'yes'}
             parameter_updates[step_id] = output_nj_phylogeny_tree_dict
             outputfh.write("Updated step id %s with the following entry:\n%s\n" % (step_id, str(output_nj_phylogeny_tree_dict)))
     return parameter_updates