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Feature head mapping - #45
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AbhirupaGhosh wants to merge 7 commits into
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1. Moved many common and utility functions to helpers.R 2. Added new manifest feature, logging all steps of workflow - Manifest is also used to identify which HMMER databases have run on a bug. - Adds extensive data provenance logging + moves databases to R user cache. 3. Removes InterProScan entirely 4. Adds Abhirupa's HMMER functionality to data_processing.R, removed runHMMER.R 5. Replaced "domain" tables/features with Pfam/COG/AMRFinder/DefenseCas 6. Added jsonlite to Imports 7. stuff Co-Authored-By: Abhirupa Ghosh <100681585+AbhirupaGhosh@users.noreply.github.com>
Introduce new function to map features to head instead of protein clusters and change the approach of reading from parquet_duckdb to only parquets.
Some reshuffling but mostly just adding support for manifest and modifying the way parameters are handled to account for manifest detection. Should be able to dynamically add databases through this, but accounting for different column names in those new DBs will take additional effort.
epbrenner
previously approved these changes
Aug 19, 2026
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Works for me! But I also added the manifest stuff to this, so somebody else needs to approve before merging.
AbhirupaGhosh
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epbrenner’s stale reviewAugust 19, 2026 21:49
The merge-base changed after approval.
AbhirupaGhosh
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Aug 19, 2026
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The integration of manifest JSON in the This PR can be merged. |
epbrenner
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Aug 20, 2026
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I still think this PR is cool. I still also think it could use one more review.
AbhirupaGhosh
dismissed
epbrenner’s stale reviewAugust 20, 2026 18:25
The merge-base changed after approval.
…database name column for HMMER generated matrices.
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Description
Introduce feature-dyad mapping in the format of two columns, where dyad is protein|gene combination.
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