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Fix #1
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@showteeth
showteeth committed Dec 28, 2023
1 parent ce966b3 commit 5846860
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Showing 2 changed files with 99 additions and 11 deletions.
1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -24,6 +24,7 @@
* Fixed bug in `ExtractZenodoMeta` (API changed).
* Fixed bug in `ShowCBDatasets` (added `--no-check-certificate` when downloading json files).
* Fixed bug in `ShowCELLxGENEDatasets`.
* Supported GEO of 10x (separate files).

-------------------

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109 changes: 98 additions & 11 deletions R/GEO.R
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Expand Up @@ -8,8 +8,9 @@
#' @param supp.idx The index of supplementary files to download. This should be consistent with \code{platform}. Default: 1.
#' @param timeout Timeout for \code{\link{download.file}}. Default: 3600.
#' @param data.type The data type of the dataset, choose from "sc" (single-cell) and "bulk" (bulk). Default: "sc".
#' @param supp.type The type of downloaded supplementary files, choose from count (count matrix file or single count matrix file)
#' and 10x (cellranger output files, contains barcodes, genes/features and matrix). Default: count.
#' @param supp.type The type of downloaded supplementary files, choose from count (count matrix file or single count matrix file),
#' 10x (cellranger output files in tar/gz supplementary files, contains barcodes, genes/features and matrix, e.g. GSE200257)
#' and 10xSingle (cellranger output files in supplementary files directly, e.g. GSE236082). Default: count.
#' @param out.folder Output folder to save 10x files. Default: NULL (current working directory).
#' @param gene2feature Logical value, whether to rename \code{genes.tsv.gz} to \code{features.tsv.gz}. Default: TRUE.
#' @param merge Logical value, whether to merge Seurat list when there are multiple 10x files (\code{supp.type} is 10x). Default: FALSE.
Expand Down Expand Up @@ -38,9 +39,14 @@
#' acce = "GSE200257", down.supp = TRUE, supp.idx = 1, supp.type = "10x",
#' out.folder = "/path/to/output/folder"
#' )
#' # need users to provide the output folder
#' GSE236082.seu <- ParseGEO(
#' acce = "GSE236082", down.supp = TRUE, supp.type = "10xSingle",
#' out.folder = "/path/to/output/folder"
#' )
#' }
ParseGEO <- function(acce, platform = NULL, down.supp = FALSE, supp.idx = 1, timeout = 3600, data.type = c("sc", "bulk"),
supp.type = c("count", "10x"), out.folder = NULL, gene2feature = TRUE, merge = TRUE, ...) {
supp.type = c("count", "10x", "10xSingle"), out.folder = NULL, gene2feature = TRUE, merge = TRUE, ...) {
# check parameters
data.type <- match.arg(arg = data.type)
supp.type <- match.arg(arg = supp.type)
Expand Down Expand Up @@ -69,7 +75,8 @@ ParseGEO <- function(acce, platform = NULL, down.supp = FALSE, supp.idx = 1, tim
return(pf.count)
} else if (data.type == "sc") {
# load seurat
if (is.null(pf.count) && supp.type == "10x") {
# if (is.null(pf.count) && supp.type == "10x") {
if (is.null(pf.count) && (supp.type == "10x" || supp.type == "10xSingle")) {
message("Loading data to Seurat!")
all.samples.folder <- dir(out.folder, full.names = TRUE)
# check file
Expand Down Expand Up @@ -443,28 +450,107 @@ ExtractGEOExpSupp10x <- function(acce, supp.idx = 1, timeout = 3600,
}
}

#' Fortmat Supplementary Files to 10x (separate files).
#'
#' @param acce GEO accession number.
#' @param timeout Timeout for \code{\link{download.file}}. Default: 3600.
#' @param out.folder Output folder to save 10x files. Default: NULL (current working directory).
#' @param gene2feature Logical value, whether to rename \code{genes.tsv.gz} to \code{features.tsv.gz}.
#' Default: TURE.
#'
#' @return NULL
#'
ExtractGEOExpSupp10xSingle <- function(acce, timeout = 3600, out.folder = NULL, gene2feature = TRUE) {
# create tmp folder
tmp.folder <- tempdir()
# get current timeout
if (!is.null(timeout)) {
message("Change Timeout to: ", timeout)
env.timeout <- getOption("timeout")
on.exit(options(timeout = env.timeout)) # restore timeout
options(timeout = timeout)
}
# download supp file
supp.down.log <- tryCatch(
expr = {
GEOquery::getGEOSuppFiles(GEO = acce, baseDir = tmp.folder)
},
error = function(e) {
print(e)
stop("You can change the timeout with a larger value.")
}
)
# get valid files
valid.pat <- "barcodes.tsv.gz$|genes.tsv.gz$|matrix.mtx.gz$|features.tsv.gz$"
all.files <- list.files(file.path(tmp.folder, acce), full.names = TRUE, pattern = valid.pat)
# change file name
if (gene2feature) {
change.name.log <- sapply(all.files, function(x) {
if (grepl(pattern = "genes.tsv.gz$", x = x)) {
new.name <- gsub(pattern = "genes.tsv.gz$", replacement = "features.tsv.gz", x = x)
file.rename(from = x, to = new.name)
}
})
all.files <- list.files(file.path(tmp.folder, acce), full.names = TRUE, pattern = valid.pat)
}
# prepare out folder
if (is.null(out.folder)) {
out.folder <- getwd()
}
# get folder
all.sample.folder <- sapply(all.files, function(x) {
# get basename and dirname
file.name <- basename(x)
dir.name <- dirname(x)
# remove file type tag
file.name <- gsub(pattern = valid.pat, replacement = "", x = file.name)
# remove possible _ and .
file.name <- gsub(pattern = "[_.]$", replacement = "", x = file.name)
file.folder <- file.path(out.folder, file.name)
})
# create folder and move file
move.file.log <- sapply(all.files, function(x) {
# get folder name
folder.name <- all.sample.folder[x]
# create folder
if (!dir.exists(folder.name)) {
dir.create(path = folder.name, recursive = TRUE)
}
new.file.name <- gsub(pattern = paste0(".*(barcodes.tsv.gz$|genes.tsv.gz$|matrix.mtx.gz$|features.tsv.gz$)"), replacement = "\\1", x = x)
# move file
copy.tag <- file.copy(from = x, to = file.path(folder.name, new.file.name))
# remove the original file
remove.tag <- file.remove(x)
copy.tag
})
message("Process 10x fiels done! All files are in ", out.folder)
}

#' Extract Raw Count Matrix from Supplementary Files or Fortmat Supplementary Files to 10x.
#'
#' @param acce GEO accession number.
#' @param supp.idx The index of supplementary files to download. Default: 1.
#' @param timeout Timeout for \code{\link{download.file}}. Default: 3600.
#' @param supp.type The type of downloaded supplementary files, choose from count (count matrix file or single count matrix file)
#' and 10x (cellranger output files, contains barcodes, genes/features and matrix). Default: count.
#' @param supp.type The type of downloaded supplementary files, choose from count (count matrix file or single count matrix file),
#' 10x (cellranger output files in tar/gz supplementary files, contains barcodes, genes/features and matrix, e.g. GSE200257)
#' and 10xSingle (cellranger output files in supplementary files directly, e.g. GSE236082). Default: count.
#' @param out.folder Output folder to save 10x files. Default: NULL (current working directory).
#' @param gene2feature Logical value, whether to rename \code{genes.tsv.gz} to \code{features.tsv.gz}. Default: TRUE.
#' Default: TURE.
#'
#' @return Count matrix (\code{supp.type} is count) or NULL (\code{supp.type} is 10x).
#'
ExtractGEOExpSuppAll <- function(acce, supp.idx = 1, timeout = 3600,
supp.type = c("count", "10x"), out.folder = NULL, gene2feature = TRUE) {
supp.type = c("count", "10x", "10xSingle"), out.folder = NULL, gene2feature = TRUE) {
if (supp.type == "count") {
count.mat <- ExtractGEOExpSupp(acce = acce, supp.idx = supp.idx, timeout = timeout)
return(count.mat)
} else if (supp.type == "10x") {
ExtractGEOExpSupp10x(acce = acce, supp.idx = supp.idx, timeout = timeout, out.folder = out.folder, gene2feature = gene2feature)
return(NULL)
} else if (supp.type == "10xSingle") {
ExtractGEOExpSupp10xSingle(acce = acce, timeout = timeout, out.folder = out.folder, gene2feature = gene2feature)
return(NULL)
}
}

Expand All @@ -477,15 +563,16 @@ ExtractGEOExpSuppAll <- function(acce, supp.idx = 1, timeout = 3600,
#' download supplementary files. If FALSE, use \code{ExpressionSet} (If contains non-integer or emoty,
#' download supplementary files automatically). Default: FALSE.
#' @param timeout Timeout for \code{\link{download.file}}. Default: 3600.
#' @param supp.type The type of downloaded supplementary files, choose from count (count matrix file or single count matrix file)
#' and 10x (cellranger output files, contains barcodes, genes/features and matrix). Default: count.
#' @param supp.type The type of downloaded supplementary files, choose from count (count matrix file or single count matrix file),
#' 10x (cellranger output files in tar/gz supplementary files, contains barcodes, genes/features and matrix, e.g. GSE200257)
#' and 10xSingle (cellranger output files in supplementary files directly, e.g. GSE236082). Default: count.
#' @param out.folder Output folder to save 10x files. Default: NULL (current working directory).
#' @param gene2feature Logical value, whether to rename \code{genes.tsv.gz} to \code{features.tsv.gz}. Default: TRUE.
#'
#' @return Count matrix (\code{supp.type} is count) or NULL (\code{supp.type} is 10x).
#' @return Count matrix (\code{supp.type} is count) or NULL (\code{supp.type} is 10x/10xSingle).
#'
ExtractGEOExp <- function(pf.obj, acce, supp.idx = 1, down.supp = FALSE, timeout = 3600,
supp.type = c("count", "10x"), out.folder = NULL, gene2feature = TRUE) {
supp.type = c("count", "10x", "10xSingle"), out.folder = NULL, gene2feature = TRUE) {
# check parameters
supp.type <- match.arg(arg = supp.type)
# download supplementary files
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