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Merge pull request #129 from umccr/sash_tidy
Sash support
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,261 @@ | ||
| #' Wf_sash R6 Class | ||
| #' | ||
| #' @description | ||
| #' Reads and writes tidy versions of files from the `sash` workflow | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' | ||
| #' #---- Local ----# | ||
| #' p1 <- "~/s3/org.umccr.data.oncoanalyser/analysis_data/SBJ05571/sash" | ||
| #' p2 <- "202408270b93455e/L2401308_L2401307" | ||
| #' p <- normalizePath(file.path(p1, p2)) | ||
| #' SubjectID <- "SBJ05571" | ||
| #' SampleID_tumor <- "MDX240307" | ||
| #' prefix <- glue("{SubjectID}__{SampleID_tumor}") | ||
| #' s1 <- Wf_sash$new(path = p, SubjectID = SubjectID, SampleID_tumor = SampleID_tumor) | ||
| #' s1$list_files(max_files = 20) | ||
| #' s1$list_files_filter_relevant(max_files = 300) | ||
| #' d <- s1$download_files(max_files = 1000, dryrun = F) | ||
| #' d_tidy <- s1$tidy_files(d) | ||
| #' d_write <- s1$write( | ||
| #' d_tidy, | ||
| #' outdir = file.path(p, "dracarys_tidy"), | ||
| #' prefix = glue("{SubjectID}_{SampleID_tumor}"), | ||
| #' format = "tsv" | ||
| #' ) | ||
| #' | ||
| #' #---- S3 ----# | ||
| #' p1 <- "s3://org.umccr.data.oncoanalyser/analysis_data/SBJ05571/sash" | ||
| #' p2 <- "202408270b93455e/L2401308_L2401307" | ||
| #' p <- file.path(p1, p2) | ||
| #' SubjectID <- "SBJ05571" | ||
| #' SampleID_tumor <- "MDX240307" | ||
| #' prefix <- glue("{SubjectID}__{SampleID_tumor}") | ||
| #' s1 <- Wf_sash$new(path = p, SubjectID = SubjectID, SampleID_tumor = SampleID_tumor) | ||
| #' s1$list_files(max_files = 20) | ||
| #' s1$list_files_filter_relevant() | ||
| #' outdir <- sub("s3:/", "~/s3", p) | ||
| #' d <- s1$download_files(outdir = outdir, max_files = 1000, dryrun = F) | ||
| #' d_tidy <- s1$tidy_files(d) | ||
| #' d_write <- s1$write( | ||
| #' d_tidy, | ||
| #' outdir = file.path(p, "dracarys_tidy"), | ||
| #' prefix = glue("{SubjectID}__{SampleID_tumor}"), | ||
| #' format = "tsv" | ||
| #' ) | ||
| #' } | ||
| #' | ||
| #' @export | ||
| Wf_sash <- R6::R6Class( | ||
| "Wf_sash", | ||
| inherit = Wf, | ||
| public = list( | ||
| #' @field SubjectID The SubjectID of the sample (needed for path lookup). | ||
| #' @field SampleID_tumor The SampleID of the tumor sample (needed for path lookup). | ||
| SubjectID = NULL, | ||
| SampleID_tumor = NULL, | ||
| #' @description Create a new Wf_sash object. | ||
| #' @param path Path to directory with raw workflow results (from GDS, S3, or | ||
| #' local filesystem). | ||
| #' @param SubjectID The SubjectID of the sample (needed for path lookup). | ||
| #' @param SampleID_tumor The SampleID of the tumor sample (needed for path lookup). | ||
| initialize = function(path = NULL, SubjectID = NULL, SampleID_tumor = NULL) { | ||
| wname <- "sash" | ||
| pref <- glue("{SubjectID}_{SampleID_tumor}") | ||
| crep <- "cancer_report/cancer_report_tables" | ||
| regexes <- tibble::tribble( | ||
| ~regex, ~fun, | ||
| glue("{pref}/{crep}/hrd/{pref}-chord\\.tsv\\.gz$"), "hrd_chord", | ||
| glue("{pref}/{crep}/hrd/{pref}-hrdetect\\.tsv\\.gz$"), "hrd_hrdetect", | ||
| glue("{pref}/{crep}/hrd/{pref}-dragen\\.tsv\\.gz$"), "hrd_dragen", | ||
| glue("{pref}/{crep}/sigs/{pref}-snv_2015\\.tsv\\.gz$"), "sigs_snv2015", | ||
| glue("{pref}/{crep}/sigs/{pref}-snv_2020\\.tsv\\.gz$"), "sigs_snv2020", | ||
| glue("{pref}/{crep}/sigs/{pref}-dbs\\.tsv\\.gz$"), "sigs_dbs", | ||
| glue("{pref}/{crep}/sigs/{pref}-indel\\.tsv\\.gz$"), "sigs_indel", | ||
| glue("{pref}/{crep}/{pref}-qc_summary\\.tsv\\.gz$"), "qcsum", | ||
| glue("{pref}/smlv_somatic/report/pcgr/{SampleID_tumor}\\.pcgr_acmg\\.grch38\\.json\\.gz$"), "pcgr_json" | ||
| ) |> | ||
| dplyr::mutate(fun = paste0("read_", .data$fun)) | ||
|
|
||
| super$initialize(path = path, wname = wname, regexes = regexes) | ||
| self$SubjectID <- SubjectID | ||
| self$SampleID_tumor <- SampleID_tumor | ||
| }, | ||
| #' @description Print details about the Workflow. | ||
| #' @param ... (ignored). | ||
| print = function(...) { | ||
| res <- tibble::tribble( | ||
| ~var, ~value, | ||
| "path", self$path, | ||
| "wname", self$wname, | ||
| "filesystem", self$filesystem, | ||
| "SubjectID", self$SubjectID, | ||
| "SampleID_tumor", self$SampleID_tumor | ||
| ) | ||
| print(res) | ||
| invisible(self) | ||
| }, | ||
| #' @description Read `pcgr.json.gz` file. | ||
| #' @param x Path to file. | ||
| read_pcgr_json = function(x) { | ||
| j <- read_jsongz_jsonlite(x) | ||
| tmb <- | ||
| j[["content"]][["tmb"]][["variant_statistic"]] %||% | ||
| j[["content"]][["tmb"]][["v_stat"]] %||% | ||
| list(tmb_estimate = NA, n_tmb = NA) | ||
| tmb <- purrr::flatten(tmb) |> | ||
| tibble::as_tibble_row() |> | ||
| dplyr::select("tmb_estimate", "n_tmb") | ||
| msi <- j[["content"]][["msi"]][["prediction"]][["msi_stats"]] | ||
| # handle nulls | ||
| msi <- msi %||% list(fracIndels = NA, predicted_class = NA) | ||
| msi <- purrr::flatten(msi) |> | ||
| tibble::as_tibble_row() |> | ||
| dplyr::select("fracIndels", "predicted_class") | ||
| metrics <- dplyr::bind_cols(msi, tmb) | ||
| return(metrics) | ||
| }, | ||
| #' @description Read `dragen.tsv.gz` cancer report hrd file. | ||
| #' @param x Path to file. | ||
| read_hrd_dragen = function(x) { | ||
| ct <- readr::cols(.default = "d", Sample = "c") | ||
| read_tsvgz(x, col_types = ct) | ||
| }, | ||
| #' @description Read `chord.tsv.gz` cancer report hrd file. | ||
| #' @param x Path to file. | ||
| read_hrd_chord = function(x) { | ||
| ct <- readr::cols_only( | ||
| p_hrd = "d", | ||
| hr_status = "c", | ||
| hrd_type = "c", | ||
| p_BRCA1 = "d", | ||
| p_BRCA2 = "d" | ||
| ) | ||
| read_tsvgz(x, col_types = ct) | ||
| }, | ||
| #' @description Read `hrdetect.tsv.gz` cancer report hrd file. | ||
| #' @param x Path to file. | ||
| read_hrd_hrdetect = function(x) { | ||
| ct <- readr::cols( | ||
| .default = "d", | ||
| sample = "c" | ||
| ) | ||
| read_tsvgz(x, col_types = ct) |> | ||
| dplyr::select(-c("sample")) | ||
| }, | ||
| #' @description Read signature cancer report file. | ||
| #' @param x Path to file. | ||
| read_sigstsv = function(x) { | ||
| ct <- readr::cols( | ||
| .default = "d", | ||
| Signature = "c" | ||
| ) | ||
| read_tsvgz(x, col_types = ct) | ||
| }, | ||
| #' @description Read `snv_2015.tsv.gz` sigs cancer report file. | ||
| #' @param x Path to file. | ||
| read_sigs_snv2015 = function(x) { | ||
| self$read_sigstsv(x) | ||
| }, | ||
| #' @description Read `snv_2020.tsv.gz` sigs cancer report file. | ||
| #' @param x Path to file. | ||
| read_sigs_snv2020 = function(x) { | ||
| self$read_sigstsv(x) | ||
| }, | ||
| #' @description Read `dbs.tsv.gz` sigs cancer report file. | ||
| #' @param x Path to file. | ||
| read_sigs_dbs = function(x) { | ||
| self$read_sigstsv(x) | ||
| }, | ||
| #' @description Read `indel.tsv.gz` sigs cancer report file. | ||
| #' @param x Path to file. | ||
| read_sigs_indel = function(x) { | ||
| self$read_sigstsv(x) | ||
| }, | ||
| #' @description Read `qc_summary.tsv.gz` cancer report file. | ||
| #' @param x Path to file. | ||
| read_qcsum = function(x) { | ||
| d <- read_tsvgz(x, col_types = readr::cols(.default = "c")) | ||
| d |> | ||
| dplyr::select("variable", "value") |> | ||
| tidyr::pivot_wider(names_from = "variable", values_from = "value") |> | ||
| dplyr::rename(MSI_mb_tmp = "MSI (indels/Mb)") |> | ||
| dplyr::mutate( | ||
| purity_hmf = sub("(.*) \\(.*\\)", "\\1", .data$Purity) |> as.numeric(), | ||
| ploidy_hmf = sub("(.*) \\(.*\\)", "\\1", .data$Ploidy) |> as.numeric(), | ||
| msi_mb_hmf = sub(".* \\((.*)\\)", "\\1", .data$MSI_mb_tmp) |> as.numeric(), | ||
| contamination_hmf = as.numeric(.data$Contamination), | ||
| deleted_genes_hmf = as.numeric(.data$DeletedGenes), | ||
| msi_hmf = sub("(.*) \\(.*\\)", "\\1", .data$MSI_mb_tmp), | ||
| tmb_hmf = sub("(.*) \\(.*\\)", "\\1", .data$TMB) |> as.numeric(), | ||
| tml_hmf = sub("(.*) \\(.*\\)", "\\1", .data$TML) |> as.numeric(), | ||
| hypermutated = ifelse("Hypermutated" %in% d$variable, .data[["Hypermutated"]], NA) |> as.character() | ||
| ) |> | ||
| dplyr::select( | ||
| qc_status_hmf = "QC_Status", | ||
| sex_hmf = "Gender", | ||
| "purity_hmf", "ploidy_hmf", "msi_hmf", "msi_mb_hmf", | ||
| "contamination_hmf", | ||
| "deleted_genes_hmf", "tmb_hmf", "tml_hmf", | ||
| wgd_hmf = "WGD", | ||
| "hypermutated" | ||
| ) | ||
| } | ||
| ) # end public | ||
| ) | ||
|
|
||
| #' sash Download Tidy and Write | ||
| #' | ||
| #' Downloads files from the `sash` workflow and writes them in a tidy format. | ||
| #' | ||
| #' @param path Path to directory with raw workflow results (from GDS, S3, or | ||
| #' local filesystem). | ||
| #' @param SubjectID The SubjectID of the sample (needed for path lookup). | ||
| #' @param SampleID_tumor The SampleID of the tumor sample (needed for path lookup). | ||
| #' @param outdir Path to output directory. | ||
| #' @param format Format of output files. | ||
| #' @param max_files Max number of files to list. | ||
| #' @param ica_token ICA access token (def: $ICA_ACCESS_TOKEN env var). | ||
| #' @param dryrun If TRUE, just list the files that will be downloaded (don't | ||
| #' download them). | ||
| #' @return List where each element is a tidy tibble of a sash file. | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' SubjectID <- "SBJ03043" | ||
| #' SampleID_tumor <- "PRJ230004" | ||
| #' p1_gds <- glue("gds://production/analysis_data/{SubjectID}/umccrise") | ||
| #' p <- file.path(p1_gds, "20240830ec648f40/L2300064__L2300063") | ||
| #' outdir <- file.path(sub("gds:/", "~/icav1/g", p)) | ||
| #' token <- Sys.getenv("ICA_ACCESS_TOKEN") | ||
| #' d <- Wf_sash_download_tidy_write( | ||
| #' path = p, SubjectID = SubjectID, SampleID_tumor = SampleID_tumor, | ||
| #' outdir = outdir, | ||
| #' dryrun = F | ||
| #' ) | ||
| #' } | ||
| #' @export | ||
| Wf_sash_download_tidy_write <- function(path, SubjectID, SampleID_tumor, | ||
| outdir, format = "rds", max_files = 1000, | ||
| ica_token = Sys.getenv("ICA_ACCESS_TOKEN"), | ||
| dryrun = FALSE) { | ||
| s <- Wf_sash$new( | ||
| path = path, SubjectID = SubjectID, SampleID_tumor = SampleID_tumor | ||
| ) | ||
| d_dl <- s$download_files( | ||
| outdir = outdir, ica_token = ica_token, | ||
| max_files = max_files, dryrun = dryrun | ||
| ) | ||
| if (!dryrun) { | ||
| d_tidy <- s$tidy_files(d_dl) | ||
| d_write <- s$write( | ||
| d_tidy, | ||
| outdir = file.path(outdir, "dracarys_tidy"), | ||
| prefix = glue("{SubjectID}__{SampleID_tumor}"), | ||
| format = format | ||
| ) | ||
| return(d_write) | ||
| } | ||
| return(d_dl) | ||
| } |
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