Feature head mapping - #45
Open
AbhirupaGhosh wants to merge 7 commits into
Open
Conversation
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
epbrenner
left a comment
epbrenner
left a comment
Contributor
There was a problem hiding this comment.
Works for me! But I also added the manifest stuff to this, so somebody else needs to approve before merging.
AbhirupaGhosh
dismissed
epbrenner’s stale review
August 19, 2026 21:49
The merge-base changed after approval.
Contributor
Author
|
The integration of manifest JSON in the This PR can be merged. |
epbrenner
previously approved these changes
Aug 20, 2026
epbrenner
left a comment
epbrenner
left a comment
Contributor
There was a problem hiding this comment.
I still think this PR is cool. I still also think it could use one more review.
AbhirupaGhosh
dismissed
epbrenner’s stale review
August 20, 2026 18:25
The merge-base changed after approval.
…database name column for HMMER generated matrices.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description
Introduce feature-dyad mapping in the format of two columns, where dyad is protein|gene combination.
What kind of change(s) are included?
Checklist
Please ensure that all boxes are checked before indicating that this pull request is ready for review.