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error "invalid mode: 'rU' " in teloclip (v. bioconda) #11

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stefankusch opened this issue Oct 30, 2023 · 0 comments · Fixed by #12
Closed

error "invalid mode: 'rU' " in teloclip (v. bioconda) #11

stefankusch opened this issue Oct 30, 2023 · 0 comments · Fixed by #12

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@stefankusch
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When installing and running teloclip through conda (Python v 3.11.5), I received the following error:

Traceback (most recent call last):
File "/home/sk893857/miniconda3/bin/teloclip", line 10, in
sys.exit(main())
^^^^^^
File "/home/sk893857/miniconda3/lib/python3.11/site-packages/teloclip/run_self.py", line 44, in main
ContigDict = teloclip.read_fai(args.refIdx)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sk893857/miniconda3/lib/python3.11/site-packages/teloclip/init.py", line 247, in read_fai
with open(path, "rU") as f:
^^^^^^^^^^^^^^^^
ValueError: invalid mode: 'rU'


note: This appears to be an invalid file read mode in Python 3. I solved this by manually replacing all instances of 'rU' with 'r' in both scripts. Maybe the conda version of teloclip needs a fix?

@Adamtaranto Adamtaranto linked a pull request Oct 30, 2023 that will close this issue
This was referenced Oct 30, 2023
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