[R] Need help to unzip files in Windows

[Rui Barradas]

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 <akwsimmo using 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 <anasjamshed1994 using 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 <akwsimmo using 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 <anasjamshed1994 using 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 using 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]]
> 
> ______________________________________________
> R-help using 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.
>