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Fix processed data exporter + add more export options - #47
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epbrenner wants to merge 2 commits into
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Allows exportProcessedData function to handle dynamic HMMER data using the manifest, removed old mention of domains, and added in a helper and exportProcessedData parameter to export a dyad feature table mapping all features linked to that dyad as a little bonus.
Updated stale documentation throughout, changed a parameter name (Total_proteins -> total_proteins), wired @AbhirupaGhosh's dyad exporter into `runDataProcessing()`, and added `exportProcessedData()` into `runDataProcessing()`.
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Updated
exportProcessedData()to use the new manifest JSON to fetch HMMER databases that were run and produce appropriate output tables, added dyad export functionality toexportProcessedData(), addedbuildDyadFeatureMap()to defaultrunDataProcessing()workflow and added option to invokeexportProcessedData()as part of the workflow.Updated some old, crusty function definitions throughout.
To-do:
Regenerate documentation properly
Test on other hardware for export functionality
Find ways to break it
To test:
prepareGenomes("Staphylococcus argenteus")or your favorite bug
runDataProcessing("data/Staphylococcus_argenteus/Sar.duckdb"), export_tabular_data = TRUE, hmmer_databases = c("COG, DefenseCas"))Check out those tables
exportProcessedData("data/Staphylococcus_argenteus/Sar.duckdb", export_formats = ("tsv", "parquet"), export_dyads = TRUE, amr_phenotype_mode = "append")And all the other wacky variants you can dream up.