Running the combine_bracken_outputs.py with Python3

[TakacsBertalan]

I was getting the following error message, when I tried to run the combine_bracken_outputs.py with Python3.6 File "/media/data/Sunbeam/sunbeam-dev/Bracken/analysis_scripts/combine_bracken_outputs.py", line 133, in main taxid = sample_counts[name].keys()[0] TypeError: 'dict_keys' object does not support indexing I suggest the following very simple fix for the issue: taxid = list(sample_counts[name].keys())[0] By changing this one line, the script becomes runnable with Python3

[jenniferlu717]

If you can make a pull request, I think I can incorporate that (as long as that still works with python2)

[Rohit-Satyam]

I think this has not been incorporated yet. I still get this error.

[rzhan186]

program worked by manually replacing the line taxid = sample_counts[name].keys()[0] in combine_bracken_outputs.py with taxid = list(sample_counts[name].keys())[0]