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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
56 stars 9 forks source link

`guess_bampe` missing for `epic2-df` #46

Closed mzytnicki closed 3 years ago

mzytnicki commented 3 years ago

Whenever I use epic2-df (version 0.0.47), I have the following error:

Traceback (most recent call last):
  File "/home/user/.local/bin/epic2-df", line 332, in <module>
    bins_counts_ko = _main(args)
  File "/home/user/.local/lib/python3.8/site-packages/epic2/main.py", line 35, in _main
    effective_genome_length, chromsizes = egl_and_chromsizes(args)
  File "epic2/src/genome_info.pyx", line 315, in epic2.src.genome_info.egl_and_chromsizes
  File "epic2/src/genome_info.pyx", line 93, in epic2.src.genome_info.find_readlength 
KeyError: 'guess_bampe'

For instance, the command generated by epic2-df -ex leads to the same error.

Correct if I am wrong, but the option --guess-bampe is now present in epic2, but not in epic2-df. As a result, the key guess_bampe is not set in args (neither True or False, simply not set).

Would this be the source of the problem?

Thanks for the help!

endrebak commented 3 years ago

I will look into it. Will probably have some time on Friday :) Sounds like your guess is correct.

endrebak commented 3 years ago

Thanks for reporting 🙏

0.0.48 is out. Does it work now?

mzytnicki commented 3 years ago

It seems that the last version for pip is still 0.0.47, so... well... I added manually the missing chunk into the code. I am not proud of it, but it seems to work fine now! I tried with and without --guess-bampe.

endrebak commented 3 years ago

Try pip install epic2 --no-cache-dir

On Thu, Jan 14, 2021 at 9:34 PM mzytnicki notifications@github.com wrote:

Closed #46 https://github.com/biocore-ntnu/epic2/issues/46.

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mzytnicki commented 3 years ago

Says:

Requirement already satisfied: epic2 in /home/login/.local/lib/python3.8/site-packages (0.0.47)

And refuse to download version 0.0.48.

endrebak commented 3 years ago

I am sorry to hear! But I suspect that is due to PyPI quirkiness. Here you see that a non-OS specific version of 0.0.48 is out on PyPI: https://pypi.org/project/epic2/#files Perhaps bioconda has it?

On Fri, Jan 15, 2021 at 7:06 PM mzytnicki notifications@github.com wrote:

Says:

Requirement already satisfied: epic2 in /home/login/.local/lib/python3.8/site-packages (0.0.47)

And refuse to download version 0.0.48.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore-ntnu/epic2/issues/46#issuecomment-761096592, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEHURUWEEQSY4MXMXLYY7XTS2B72LANCNFSM4WALMNYQ .

mzytnicki commented 3 years ago

My fault! I forgot the --upgrade flag... I have now the version 0.0.48, which works like a charm. Thanks!