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refactor(dada2): use base R for taxonomy CSV assembly #61
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JoshuaJewell
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hyperpolymath:repair/dada2-base-r
Oct 17, 2026
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| # Regression checks for CSV assembly, without loading DADA2 or dplyr. | ||
| # Run from the repository root: Rscript --vanilla test/unit/test_dada2_tables.R | ||
| expressions <- parse("src/pipeline/dada2/dada2_functions.r") | ||
| wanted <- c("base_left_join", "write_taxa_table", "write_combined_table") | ||
| loaded <- character() | ||
| for (expr in expressions) { | ||
| if (is.call(expr) && identical(expr[[1]], as.name("<-")) && | ||
| is.symbol(expr[[2]]) && as.character(expr[[2]]) %in% wanted) { | ||
| eval(expr) | ||
| loaded <- c(loaded, as.character(expr[[2]])) | ||
| } | ||
| } | ||
| stopifnot(setequal(loaded, wanted)) | ||
|
|
||
| # Unsorted keys, repeated matches, unmatched rows, overlapping column names, | ||
| # NA keys, and helper-column name collisions must preserve the intended order. | ||
| x <- data.frame(value = 1:4, key = c("b", "a", "z", NA), | ||
| .left_join_position = 11:14) | ||
| y <- data.frame(key = c("a", "b", "b", NA), value = 21:24, | ||
| .right_join_position = 31:34) | ||
| got <- base_left_join(x, y, "key") | ||
| stopifnot(identical(got$key, c("b", "b", "a", "z", NA_character_)), | ||
| identical(got$value.x, c(1L, 1L, 2L, 3L, 4L)), | ||
| identical(got$value.y, c(22L, 23L, 21L, NA_integer_, 24L)), | ||
| identical(names(got), c("value.x", "key", ".left_join_position", | ||
| "value.y", ".right_join_position"))) | ||
| stopifnot(nrow(base_left_join(x[FALSE, ], y, "key")) == 0L, | ||
| nrow(base_left_join(x, y[FALSE, ], "key")) == nrow(x)) | ||
| # Multiple keys: matching only one component must not produce a match. | ||
| a <- data.frame(id = c("a", "a"), key = c("x", "y"), value = 1:2) | ||
| b <- data.frame(id = c("a", "b"), key = c("y", "x"), other = 3:4) | ||
| stopifnot(identical(base_left_join(a, b, c("id", "key"))$other, | ||
| c(NA_integer_, 3L))) | ||
|
|
||
| # Rank names and their suffixed variants are also valid sample IDs. | ||
| # Repeated suffixing must preserve both the taxonomy strings and count columns. | ||
| tax_collision <- data.frame(Sequence = c("AA", "GG"), Species = c("taxA", "taxG")) | ||
| count_collision <- data.frame(Sequence = c("GG", "AA"), Species = c(10L, 20L), | ||
| Species.x = c(30L, 40L), Species.x.x = c(50L, 60L)) | ||
| collision <- base_left_join(tax_collision, count_collision, "Sequence") | ||
| stopifnot(identical(names(collision), | ||
| c("Sequence", "Species.x.x.x", "Species.y", "Species.x", "Species.x.x")), | ||
| identical(collision[[2]], c("taxA", "taxG")), | ||
| identical(collision[[3]], c(20L, 10L)), | ||
| identical(collision[[4]], c(40L, 30L)), | ||
| identical(collision[[5]], c(60L, 50L))) | ||
|
|
||
| # Fixed expected CSV bytes cover every writer output, including non-syntactic | ||
| # sample names and an unmatched taxonomy row. No sequencing dependencies needed. | ||
| out <- tempfile("dada2-tables-") | ||
| dir.create(out) | ||
| index <- data.frame(SeqName = c("ASV3", "ASV1", "ASV2"), | ||
| Sequence = c("TT", "GG", "AA")) | ||
| tax <- matrix(c("G", "A"), ncol = 1, | ||
| dimnames = list(c("GG", "AA"), "Kingdom")) | ||
| boot <- matrix(c(90L, 80L), ncol = 1, dimnames = dimnames(tax)) | ||
| taxa <- write_taxa_table(tax, boot, index, out, "taxonomy") | ||
| counts <- matrix(c(1L, 2L, 3L, 4L, 5L, 6L), nrow = 2, | ||
| dimnames = list(c("sample-1", "sample 2"), c("AA", "TT", "GG"))) | ||
| write_combined_table(taxa, index, counts, out, "tax_counts.csv", "asv_counts.csv") | ||
| expected <- list( | ||
| taxonomy.csv = c("SeqName,Sequence,Kingdom", "ASV3,TT,NA", "ASV1,GG,G", "ASV2,AA,A"), | ||
| taxonomy_bootstraps.csv = c("SeqName,Sequence,Kingdom_boot", "ASV3,TT,NA", "ASV1,GG,90", "ASV2,AA,80"), | ||
| taxonomy_combined.csv = c("SeqName,Sequence,Kingdom,Kingdom_boot", "ASV3,TT,NA,NA", "ASV1,GG,G,90", "ASV2,AA,A,80"), | ||
| tax_counts.csv = c("SeqName,Sequence,Kingdom,sample-1,sample 2", "ASV3,TT,NA,3,4", "ASV1,GG,G,5,6", "ASV2,AA,A,1,2"), | ||
| asv_counts.csv = c("SeqName,Sequence,sample-1,sample 2", "ASV3,TT,3,4", "ASV1,GG,5,6", "ASV2,AA,1,2") | ||
| ) | ||
| for (name in names(expected)) { | ||
| path <- file.path(out, name) | ||
| bytes <- readBin(path, "raw", n = file.info(path)$size) | ||
| stopifnot(identical(bytes, charToRaw(paste0(paste(expected[[name]], collapse = "\n"), "\n")))) | ||
| } | ||
| unlink(out, recursive = TRUE) | ||
| cat("DADA2 join and five CSV fixtures passed\n") |
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