ROSE Algorithm: Error when importing upper and join from string

Question

[mropri]

Hello,

I am trying to run the ROSE algorithm created by the young lab, url here:

http://younglab.wi.mit.edu/super_enhancer_code.html

Specifically, I am running the ROSE_main.py script: http://younglab.wi.mit.edu/super_enhancer_code.html

When I run the script in ubuntu, my python version 3.7.6, I get an error stating the following:

Traceback (most recent call last):

File "ROSE_main.py", line 19, in <module>

from string import uppercase, join ImportError: cannot import name 'uppercase' from 'string' (/network/rit/lab/herschkolab/Ali/miniconda3/lib/python3.7/string.py)**

So as you can see, when importing upper, join from string, the script gets an error. I was hoping someone could help me understand why I get that error and how to fix it. Any help is appreciated. Thank you!

Answer 1

[ATpoint]

From the website:

Developed using Python 2.7.3, R 2.15.3, and SAMtools 0.1.18

You have python3, it needs python2. I suggest you create a separate environment with conda and install python2 on it.

[mropri]

Thank you, will try that

Answer 2

[jared.andrews07]

There is also a python3 updated version here (and likely a few other repos as well).

[mropri]

Thanks for the reply, will try this version as well.