CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
69 lines
1.9 KiB
R
Executable File
69 lines
1.9 KiB
R
Executable File
#!/usr/bin/env Rscript
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library(SummarizedExperiment)
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## Create SummarizedExperiment (se) object from Salmon counts
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args <- commandArgs(trailingOnly = TRUE)
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if (length(args) < 2) {
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stop("Usage: salmon_se.r <coldata> <counts> <tpm>", call. = FALSE)
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}
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coldata <- args[1]
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counts_fn <- args[2]
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tpm_fn <- args[3]
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tx2gene <- args[4]
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info <- file.info(tx2gene)
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if (info$size == 0) {
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tx2gene <- NULL
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} else {
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rowdata <- read.csv(tx2gene, sep = "\t", header = FALSE)
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colnames(rowdata) <- c("tx", "gene_id", "gene_name")
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tx2gene <- rowdata[, 1:2]
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}
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counts <- read.csv(counts_fn, row.names = 1, sep = "\t")
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counts <- counts[, 2:ncol(counts), drop = FALSE] # remove gene_name column
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tpm <- read.csv(tpm_fn, row.names = 1, sep = "\t")
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tpm <- tpm[, 2:ncol(tpm), drop = FALSE] # remove gene_name column
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if (length(intersect(rownames(counts), rowdata[["tx"]])) > length(intersect(rownames(counts), rowdata[["gene_id"]]))) {
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by_what <- "tx"
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} else {
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by_what <- "gene_id"
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rowdata <- unique(rowdata[, 2:3])
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}
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if (file.exists(coldata)) {
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coldata <- read.csv(coldata, sep = "\t")
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coldata <- coldata[match(colnames(counts), coldata[, 1]), ]
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coldata <- cbind(files = fns, coldata)
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} else {
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message("ColData not avaliable ", coldata)
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coldata <- data.frame(files = colnames(counts), names = colnames(counts))
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}
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rownames(coldata) <- coldata[["names"]]
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extra <- setdiff(rownames(counts), as.character(rowdata[[by_what]]))
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if (length(extra) > 0) {
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rowdata <- rbind(
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rowdata,
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data.frame(
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tx = extra,
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gene_id = extra,
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gene_name = extra
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)[, colnames(rowdata)]
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)
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}
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rowdata <- rowdata[match(rownames(counts), as.character(rowdata[[by_what]])), ]
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rownames(rowdata) <- rowdata[[by_what]]
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se <- SummarizedExperiment(
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assays = list(counts = counts, abundance = tpm),
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colData = DataFrame(coldata),
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rowData = rowdata
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)
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saveRDS(se, file = paste0(tools::file_path_sans_ext(counts_fn), ".rds"))
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