Code

Introduce user-provided hmms#327

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oschwengers merged 21 commits intomainoschwengers/bakta:mainfrom feature-user-hmmsoschwengers/bakta:feature-user-hmmsCopy head branch name to clipboardOct 10, 2024

+2,529-52

Commits

Commits on Sep 24, 2024

• fix table in readme

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  561a676

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• add hmm parameter

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  3b4da1c

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• bump PyHMMER dependency to 0.10.14

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  36eb4cb

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• introduce MIN_HMM_EVALUE constant

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• implement HMM search

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• add tests

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  091d0b0

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• adjust ranks of user-provided proteins and HMMs

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• print user hmm parameter to stdout

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  4029e04

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• add hmms to readme

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Commits on Sep 25, 2024

• Merge branch 'main' into feature-user-hmms

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Commits on Sep 30, 2024

• remove orf debug print

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Commits on Oct 2, 2024

• finish user-hmm feature

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  0e802d6

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• polish readme

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• add a second test HMM with short description format

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  7e50f98

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• discard hmm hit source

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• refactor expert hit annotation selection

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• take into account annotation score to rank/score equal expert hits

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Commits on Oct 9, 2024

• bump PyHMMER version to 0.10.15

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  3fdcf83

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• Merge branch 'main' into feature-user-hmms

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  598650b

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• add hmm to bulk proteins script

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  bc8a554

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• add feature inference to proteins script

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