Avoids error 'gzip: stdout: No space left on device' (https://github.com/Rdatatable/data.table/issues/717#issuecomment-226038307)
Peter Hickey authored on 04/07/2018 13:24:07
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@@ -46,7 +46,7 @@ importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement") |
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importFrom(utils, "read.delim") |
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importFrom(BSgenome, "vmatchPattern") |
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importFrom(tools, "file_path_as_absolute") |
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-importFrom(R.utils, "isGzipped") |
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+importFrom(R.utils, "isGzipped", "gunzip") |
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## |
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## Exporting |
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@@ -94,65 +94,72 @@ |
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} |
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ptime1 <- proc.time() |
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# TODO: Make copy if isGzipped() to avoid dependency on R.utils? |
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+ # TODO: Use isCompressedFile() and decompressFile(). |
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if (isGzipped(file)) {
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- sysname <- Sys.info()[["sysname"]] |
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- if (sysname == "Linux") {
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- input <- sprintf("zcat %s", shQuote(file))
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- } else if (sysname == "Darwin") {
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- # macOS/OS X needs a different command; see |
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- # https://github.com/Rdatatable/data.table/issues/717#issuecomment-140028670 |
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- input <- sprintf("zcat < %s", shQuote(file))
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- } else {
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- # TODO: Support other OSs (e.g, Windows, sunOS) |
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- warning( |
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- "Unable to find 'zcat' for use with 'data.table::fread()'.\n", |
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- "Falling back to 'utils::read.table()'.") |
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- is_zcat_available <- FALSE |
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- } |
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- # TODO: Gracefully handle situation where user incorrectly sets |
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- # `is_zcat_available = TRUE` and it consequently fails. |
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- if (is_zcat_available) {
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- x <- fread( |
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- input = input, |
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- sep = "\t", |
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- header = FALSE, |
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- verbose = subverbose, |
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- drop = drop, |
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- colClasses = colClasses, |
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- col.names = col.names, |
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- # TODO: Check remainder of these arguments are optimal. |
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- # TODO: Add `key` argument? Check other arguments available in |
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- # fread(). |
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- quote = "", |
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- strip.white = FALSE, |
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- showProgress = as.logical(verbose), |
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- nThread = nThread) |
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- } else {
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- x <- read.table( |
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- file = file, |
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- header = FALSE, |
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- sep = "\t", |
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- quote = "", |
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- col.names = col.names, |
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- colClasses = colClasses, |
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- strip.white = FALSE) |
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- setDT(x) |
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- } |
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- } else {
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- x <- fread( |
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- file = file, |
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- sep = "\t", |
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- header = FALSE, |
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- verbose = subverbose, |
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- drop = drop, |
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- colClasses = colClasses, |
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- col.names = col.names, |
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- # TODO: Check remainder of these arguments are optimal. |
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- quote = "", |
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- strip.white = FALSE, |
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- showProgress = as.logical(verbose), |
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- nThread = nThread) |
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+ message( |
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+ "[.readBismarkAsDT] Gunzipping file '", file, "' to tempfile().") |
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+ |
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+ file <- gunzip( |
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+ filename = file, |
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+ destname = tempfile(), |
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+ remove = FALSE) |
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} |
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+ # sysname <- Sys.info()[["sysname"]] |
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+ # if (sysname == "Linux") {
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+ # input <- sprintf("zcat %s", shQuote(file))
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+ # } else if (sysname == "Darwin") {
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+ # # macOS/OS X needs a different command; see |
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+ # # https://github.com/Rdatatable/data.table/issues/717#issuecomment-140028670 |
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+ # input <- sprintf("zcat < %s", shQuote(file))
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+ # } else {
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+ # # TODO: Support other OSs (e.g, Windows, sunOS) |
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+ # warning( |
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+ # "Unable to find 'zcat' for use with 'data.table::fread()'.\n", |
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+ # "Falling back to 'utils::read.table()'.") |
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+ # is_zcat_available <- FALSE |
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+ # } |
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+ # TODO: Gracefully handle situation where user incorrectly sets |
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+ # `is_zcat_available = TRUE` and it consequently fails. |
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+ # if (is_zcat_available) {
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+ # x <- fread( |
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+ # input = input, |
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+ # sep = "\t", |
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+ # header = FALSE, |
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+ # verbose = subverbose, |
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+ # drop = drop, |
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+ # colClasses = colClasses, |
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+ # col.names = col.names, |
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+ # # TODO: Check remainder of these arguments are optimal. |
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+ # # TODO: Add `key` argument? Check other arguments available in |
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+ # # fread(). |
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+ # quote = "", |
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+ # strip.white = FALSE, |
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+ # showProgress = as.logical(verbose), |
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+ # nThread = nThread) |
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+ # } else {
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+ # x <- read.table( |
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+ # file = file, |
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+ # header = FALSE, |
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+ # sep = "\t", |
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+ # quote = "", |
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+ # col.names = col.names, |
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+ # colClasses = colClasses, |
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+ # strip.white = FALSE) |
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+ # setDT(x) |
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+ # } |
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+ x <- fread( |
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+ file = file, |
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+ sep = "\t", |
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+ header = FALSE, |
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+ verbose = subverbose, |
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+ drop = drop, |
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+ colClasses = colClasses, |
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+ col.names = col.names, |
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+ # TODO: Check remainder of these arguments are optimal. |
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+ quote = "", |
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+ strip.white = FALSE, |
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+ showProgress = as.logical(verbose), |
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+ nThread = nThread) |
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# Construct the result ----------------------------------------------------- |
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