Hello,
Are you looking for what follows Andrew's code below to download and
untar the files?
read_one_gz_file <- function(x, path){
fl <- file.path(path, x)
tryCatch({
read.table(zz <- gzfile(fl))
},
warning = function(w) w,
error = function(e) e
)
}
URL <-
"https://ftp.ncbi.nlm.nih.gov/geo/series/GSE162nnn/GSE162562/suppl/GSE162562_RAW.tar";
FILE <- file.path(tempdir(), basename(URL))
utils::download.file(URL, FILE, mode = "wb")
utils::untar(FILE, exdir = dirname(FILE))
fls <- list.files(path = dirname(FILE), pattern = "\\.gz$")
length(fls)
#[1] 108
data_list <- lapply(fls, read_one_gz_file, path = dirname(FILE))
length(data_list)
#[1] 108
head(data_list[[1]])
# V1 V2
#1 A1BG 4
#2 A1BG-AS1 52
#3 A1CF 12
#4 A2M 645
#5 A2M-AS1 113
#6 A2ML1 21
I don't understand what you mean by to aggregate the files but if you
want them all in one df, maybe this will do it.
sapply(data_list, ncol) # All files have 2 columns
# create a column with the original dataset name
data_list <- lapply(seq_along(data_list), function(i){
dftmp <- data_list[[i]]
dftmp$dataset <- sub("\\.txt\\.gz$", "", fls[i])
dftmp
})
# put all data sets in one data.frame
df1 <- do.call(rbind, data_list)
dim(df1) # Over 2.8 million rows, 3 columns
head(df1) # see the first 6 rows
# V1 V2 dataset
#1 A1BG 4 GSM4954457_A_1_Asymptom
#2 A1BG-AS1 52 GSM4954457_A_1_Asymptom
#3 A1CF 12 GSM4954457_A_1_Asymptom
#4 A2M 645 GSM4954457_A_1_Asymptom
#5 A2M-AS1 113 GSM4954457_A_1_Asymptom
#6 A2ML1 21 GSM4954457_A_1_Asymptom
Hope this helps,
Rui Barradas
Às 01:16 de 24/08/21, Anas Jamshed escreveu:
sir after that I want to run:
#get the list of sample names
GSMnames <- t(list.files("~/Desktop/GSE162562_RAW", full.names = F))
#remove .txt from file/sample names
GSMnames <- gsub(pattern = ".txt", replacement = "", GSMnames)
#make a vector of the list of files to aggregate
files <- list.files("~/Desktop/GSE162562_RAW", full.names = TRUE)
but it is not running as after running utils::untar(FILE, exdir =
dirname(FILE)) it creates another 108 archieves
On Tue, Aug 24, 2021 at 2:03 AM Andrew Simmons <akwsi...@gmail.com> wrote:
Hello,
I tried downloading that file using 'utils::download.file' (which worked),
but then continued to complain about "damaged archive" when trying to use
'utils::untar'. However, it seemed to work when I downloaded the archive
manually. Finally, the solution I found is that you have to specify the
mode in which you're downloading the file. Something like:
URL <- "
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE162nnn/GSE162562/suppl/GSE162562_RAW.tar
"
FILE <- file.path(tempdir(), basename(URL))
utils::download.file(URL, FILE, mode = "wb")
utils::untar(FILE, exdir = dirname(FILE))
worked perfectly for me. It seems to also work still on Ubuntu, but you
can let us know if you find it doesn't. I hope this helps!
On Mon, Aug 23, 2021 at 3:20 PM Anas Jamshed <anasjamshed1...@gmail.com>
wrote:
I am trying this URL: "
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE162nnn/GSE162562/suppl/GSE162562_RAW.tar
"
but it is not giving me any file
On Mon, Aug 23, 2021 at 11:42 PM Andrew Simmons <akwsi...@gmail.com>
wrote:
Hello,
I don't think you need to use a system command directly, I think
'utils::untar' is all you need. I tried the same thing myself, something
like:
URL <- "https://exiftool.org/Image-ExifTool-12.30.tar.gz";
FILE <- file.path(tempdir(), basename(URL))
utils::download.file(URL, FILE)
utils::untar(FILE, exdir = dirname(FILE))
and it makes a folder "Image-ExifTool-12.30". It seems to work perfectly
fine in Windows 10 x64 build 19042. Can you send the specific file (or
provide a URL to the specific file) that isn't working for you?
On Mon, Aug 23, 2021 at 12:53 PM Anas Jamshed <anasjamshed1...@gmail.com>
wrote:
I have the file GSE162562_RAW. First I untar them
by untar("GSE162562_RAW.tar")
then I am running like:
system("gunzip ~/Desktop/GSE162562_RAW/*.gz")
This is running fine in Linux but not in windows. What changes I
should make to run this command in windows as well
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
