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' or 'untar' will fail
# this is where we put the downloaded files
exdir <- path.expand("~/GSE162562_RAW")
dir.create(exdir, showWarnings = FALSE)
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 = exdir)
unlink(FILE, recursive = TRUE, force = TRUE)
# 'files' is the full path to the downloaded files
# attribute 'names' is the basename with '.txt.gz' removed from the end
files <- list.files(exdir, full.names = TRUE)
names(files) <- sub("\\.txt\\.gz$", "", basename(files))
# R can open compressed files without decompressing beforehand
print(utils::read.table(files[[1]], sep = "\t"))
print(utils::read.delim(files[[2]], header = FALSE))
Does this work better than before for you?
On Mon, Aug 23, 2021 at 8:16 PM Anas Jamshed <anasjamshed1...@gmail.com>
wrote:
> 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
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>>>>
>>>>
[[alternative HTML version deleted]]
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