HMM model load speed

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#101 2026年4月22日に作成コメント 2 件リアクション 0 件担当者 0 名 GitHub で見る

question

説明

I noticed in my own work that the pyhmmer HMMFile loading interface is not particularly performant. It's a hacky fix, but:

import io

with open(hmmfile, 'rb') as fh:
with HMMFile(io.BytesIO(fh.read()) as hmm_file:
...

Is about 20-50x faster than using the HMMFile parser directly on the file path on my platform. I'm on WSL - it could be wierdness that way.

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