Read specific file from tar.gz in R

Question

I have a large tar.gz file (>2GB) from which I want to read a specific .dat file in R without unzipping the original tar.gz file.

I tried to follow this post as follows:

p35_data_path <- "~/P35_fullset.tar.gz" 
file.exists(p35_data_path) #TRUE

# Try to readin foldera/class1/mydata.dat from the zip file
mydata <- read.table(unz(p35_data_path
                       , "foldera/class1/mydata.dat"))

When I run the above I get a read.table error as

Error in open.connection(file, "rt") : cannot open the connection
In addition: Warning message:
In open.connection(file, "rt") :
  cannot open zip file '~/P35_fullset.tar.gz'

The "~/P35_fullset.tar.gz" file exists. And the specific file within it definitely exists foldera/class1/mydata.dat .

Could anyone please assist in rectifying this?

Answer 1

da < -untar(Tarfile, files = NULL, list = TRUE, exdir = ".",compressed = "gzip") # this is for listing the files under TAR

da < -as.data.table(da) # save listed files as datatable 

Then use your own filter technique to filtes the files like I did and saved in Name :

g <- c(da$Name)`  # then list the names

untar(Tarfile, files = g, list = FALSE, exdir = "exportRQA",compressed = "gzip") # This is finally the command for extracting the specific files.

Answer 2

Using library(archive) one can read in a particular csv file within an archive without having to UNZIP it first :

library(archive)
library(readr)
read_csv(archive_read("~/P35_fullset.tar.gz", file = 1), col_types = cols())

(adjust file=XX as appropriate)

Answer 3

You should be able to unpack the archive with base R's untar() :

p35_data_path <- "~/P35_fullset.tar.gz" 
file.exists(p35_data_path) #TRUE

# Try to readin foldera/class1/mydata.dat from the .tar.gz file
untar(p35_data_path, "foldera/class1/mydata.dat")  # this extracts the file from archive
mydata <- read.table("foldera/class1/mydata.dat")  # so you can read it

The file is extracted inside the folder, however, you can specify where to extract it. See documentation for more info.