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IEDB / PEPMatch

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Fail to import hamming #6

Closed Hayfabm closed 4 months ago

Hayfabm commented 4 months ago

Hi,

I tried to use the following script to get the mismatching output:

from pepmatch import Preprocessor, Matcher

Preprocessor('proteomes/human.fasta').pickle_proteome(k = 3)

Matcher( # 3 mismatches, k = 3
  'queries/neoepitopes-test.fasta', 'proteomes/human.fasta', 3, 3
).match()

I got an issue when importing hamming says ModuleNotFoundError: No module named 'pepmatch.hamming' Is there anything to fix?

Thanks a lot,

danielmarrama commented 4 months ago

Hello, @Hayfabm, which OS are you using? Did you pip install pepmatch or trying running from the source code?

Hayfabm commented 4 months ago

Hello @danielmarrama, I am currently testing my input peptide on Linux using source code from the cloned repository. Let me know if you need further details!

danielmarrama commented 4 months ago

Ok, I see. So, there is a C extension called hamming.c which builds when you pip install pepmatch - so it's highly recommended you do that. Try that and see if you can get it working.

Hayfabm commented 4 months ago

Thanks a lot, it works fine using the pip install pepmatch, either for exact or mismatch examples.

danielmarrama commented 4 months ago

Great!