Replacing InterProScan with HMMER + .json manifest - #44
Draft
epbrenner wants to merge 1 commit into
Draft
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>
Contributor
Author
|
To-do:
|
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Lots of changes.
To test:
source("R/helpers.R")source("R/data_curation.R")source("R/data_processing.R")prepareGenomes("Staphylococcus epidermidis")runDataProcessing("data/Staphylococcus_epidermidis/Sep.duckdb")In the
data/Staphylococcus_epidermidisdirectory, you will also find a .json manifest generated that logs a bunch of stuff. Check it out.