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althonos avatar althonos commented on June 14, 2024 1

So at the moment the window_length option was only used in the builder to build new HMMs, so it was completely ignored when nhmmer was called with pre-built HMMs. I'll work on a patch but that needs a bit of refactoring.

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moshi4 avatar moshi4 commented on June 14, 2024 1

I am closing this issue as I have released v0.2.0 which fixes the problem. Thanks for your great contribution 😃

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moshi4 avatar moshi4 commented on June 14, 2024

Hi @althonos, thanks for your comment.

In nhmmer, there is a difference in E-value depending on whether --w_length is set or not. On the other hand, pyhmmer.nhmmer does not have any difference in E-value depending on the window_length setting of the Builder class.

The following is the data to reproduce the result of nhmmer and pyhmmer.nhmmer.

nhmmer_vs_pyhmmer.nhmmer_diff.zip

bash nhmmer_example.sh and python pyhmmer.nhmmer_example.py commands output the results with and without window_length setting, respectively.

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althonos avatar althonos commented on June 14, 2024

Thanks!

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