but the point is that where should I start from now
On Tue, Aug 24, 2021 at 7:43 AM Andrew Simmons <akwsi...@gmail.com> 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 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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