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Replace HMMER with PyHMMER #219

Merged
merged 5 commits into from
Aug 11, 2023
Merged

Replace HMMER with PyHMMER #219

merged 5 commits into from
Aug 11, 2023

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jhahnfeld
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PyHMMER provides bindings to HMMER3 and allows functions like hmmsearch to be used directly in Python without temporary files.
It is faster compared to HMMER because of a new parallelization model and provides identical results.

oschwengers
oschwengers requested changes Jun 26, 2023
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@oschwengers oschwengers mentioned this pull request Jun 27, 2023
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@oschwengers oschwengers self-assigned this Aug 11, 2023
@oschwengers oschwengers added the enhancement New feature or request label Aug 11, 2023
@oschwengers oschwengers added this to the v1.9.0 milestone Aug 11, 2023
@oschwengers oschwengers merged commit 3415e89 into oschwengers:main Aug 11, 2023
oschwengers added a commit that referenced this pull request Aug 11, 2023
@oschwengers
tweak depdendency checks finding Pyrodigal & Pyhmmer versions #219
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Now, that @althonos made a clear statement, we're confident to use Pyhmmer in Bakta's production code.

@oschwengers oschwengers changed the title Replace hmmer with py hmmer Replace HMMER with PyHMMER Nov 17, 2023
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@oschwengers oschwengers oschwengers approved these changes

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enhancement New feature or request
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@jhahnfeld @oschwengers