Updated python issues - Githubissues

elizabethmcd / metabolisHMM

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs

GNU General Public License v3.0

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Updated python issues #60

Closed susheelbhanu closed 3 months ago

susheelbhanu commented 3 months ago

Hi,

I'm running the tool and coming across the below issue:

Traceback (most recent call last):
  File "/hdd0/susbus/tools/conda_env/359b7172c00f55ffb49ceca1140d208f_/bin/summarize-metabolism", line 162, in <module>
    with open(result, "rU") as input:

I'm running python=3.12.4, and from documentation, it looks like the 'U' is no longer needed starting from python=3.11. I'm testing the run to see if removing the 'U' from 'rU' will work, but just a heads-up!

Best, Susheel

susheelbhanu commented 3 months ago

Update

There were a few other tweaks that were needed, given the updated python and pandas versions, but minor ones.
I modified the original summarize-metabolism script and am attaching it here, should you want to see the changes. summarize-metabolism.py.txt