Update regex patterns for feature ID extraction#9
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AbhirupaGhosh wants to merge 9 commits intomainfrom
Closed
Update regex patterns for feature ID extraction#9AbhirupaGhosh wants to merge 9 commits intomainfrom
AbhirupaGhosh wants to merge 9 commits intomainfrom
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epbrenner
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Jan 28, 2026
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Lots of reformatting, so this is going to take me a little longer than I expected, but the regex parse fix looks appropriate. Will test tomorrow to confirm and then approve or fix as needed. Thanks for getting to the bottom of this latest quirk.
| DBI::dbExecute( | ||
| con, | ||
| glue::glue('CREATE TABLE IF NOT EXISTS {meta_table} ( | ||
| glue::glue("CREATE TABLE IF NOT EXISTS {meta_table} ( |
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I can run this in the morning, but I think DuckDB requires single quotes for these strings to be interpreted as strings, and if we're gluing this into a command then double quotes might not work properly. Will check.
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| proteinID = stringr::str_extract(value, "^fig\\|[0-9]+\\.[0-9]+\\.peg(?:sc)?\\.[0-9]+"), | ||
| locus_tag = stringr::str_match(value, "peg(?:sc)?\\.[0-9]+\\|([^\\s]+)")[, 2], |
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Makes sense as a fix. Again, will run ASAP and confirm before approving.
Rename the original cleanData to cleanMetaData and add roxygen skeleton. Introduce a writeCompressedParquet helper and export cleaned metadata, AMR phenotype, genome data and original metadata to compressed Parquet files, then create a separate DuckDB (parquet-backed) with views for metadata, amr_phenotype, genome_data and original_metadata. Reintroduce a new cleanData function focused on feature matrices (genes/proteins/domains/etc.) that writes feature tables to Parquet and creates corresponding views; remove duplicated metadata parquet exports from the feature-matrix flow. Minor whitespace and path-handling adjustments to normalize paths and ensure output directories exist.
Fixed trailing zero bug, fixed FTP timeout bug (?), fixed empty files hanging downloads, fixed imbalanced genome data sets (e.g., no .fna, yes .faa, yes .gff)
Added a function to parse CD-HIT .clstr output into a long-format mapping of clusters to member feature ids. Updated database writing logic to include the new protein members table.
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fixing #8
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