Comments (4)
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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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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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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Thanks!
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