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.ncb
but the point is that where should I start from now
On Tue, Aug 24, 2021 at 7:43 AM Andrew Simmons wrote:
> Hello,
>
>
> I see what you're saying that the .tar archive contains many more
> compressed files, but that's not necessarily a problem. R can read directly
> from a compressed file withou
Hello,
I see what you're saying that the .tar archive contains many more
compressed files, but that's not necessarily a problem. R can read directly
from a compressed file without having to decompress it beforehand. I
modified my code to look a little more like yours:
# need to do 'path.expand'
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(
There are some differences in R, between Windows and Linux.
You could try the 'shell' command instead.
#On Windows
?shell
On Tue, Aug 24, 2021 at 4:53 AM Anas Jamshed wrote:
>
> I have the file GSE162562_RAW. First I untar them
> by untar("GSE162562_RAW.tar")
> then I am running like:
> system(
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
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 wrote:
> Hello,
>
>
> I don't think you need to use a system command directly, I think
> 'utils::untar'
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::
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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