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I have a directory which consists of multiple sub-directories. Each subdirectory has a tar.gz file which on untar gives two files namely R1.fastq and R2.fastq. I want to untar the tar file and compress R1.fastq and R2.fastq immediately after piping,and save the output of each sub-directories into another SINGLE directory.

 sourcedir=/sdir
 destdir=/ddir

 for f in $sourcedir/*; do
    fbase=${f##*/}   
    echo "Inside $fbase"
 tar -xvf $f/*.gz |gzip -n9 $f/*.fastq > $destdir/
done

I wrote the above code but it goes until the echo command.

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    You cannot save the files from all the subdirectories to the same directory if the files have the same names. You should give an example of the (extracted) files in at least two subdirectories and should show the desired result. – Hauke Laging Jan 27 '15 at 2:50
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The $f/*.fastq doesn't match anything by the time that line gets invoked. But the major problem is that tar doesn't extract to stdout, it creates files (there would need to be some way to tell the 'receiving' on the other end of the pipe that one file ends and the other starts, and there isn't at least not with tar).

So when using tar you have to let tar create the files and then gzip the created files afterwards.

If the files fit in memory you can write a quick script in Python using tarfile and gzip modules and never let the uncompressed code touch the disc. IIRC the individual files are completely extracted, so for this to work they have to fit in memory.

  • R1.fastq and R2.fastq are both in 1 tar.gz file,and should be decompressed on untar,and compressed into individual .gz files.the above code does not work – Ron Jan 26 '15 at 20:48
  • @Ron That is contrary to what the question says. There you state that you decompress. Please update your question so that is correctly describes what you want to happen. – Anthon Jan 26 '15 at 20:54
  • my bad.I have updated the question.It was a mistake on my part – Ron Jan 26 '15 at 20:58
  • i have updated the code which I want but its not running – Ron Jan 26 '15 at 21:25
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The general approach is to read the file names from the archive (unless they are always the same) and then have tar extract only one file at a time. GNU tar has the option --to-stdout which prevents it from writing a file. Without that you would need a FIFO for each file name.

> tar -tf subdir.tar.gz
R1.fastq
R1.fastq

tar -xf subdir.tar.gz --to-stdout R1.fastq | gzip -n9 >/path/to/R1.fastq.gz
tar -xf subdir.tar.gz --to-stdout R2.fastq | gzip -n9 >/path/to/R2.fastq.gz
  • i didn't get how the same command tar -xf subdir.tar.gz would --to-stdout to different files.Do i need to do pattern matching while extracting? – Ron Jan 27 '15 at 16:11
  • @Ron It's not the same. Look better. – Hauke Laging Jan 27 '15 at 17:58
  • @Ron, look closer. The tar commands are indeed going to stdout, but that is then piped into gzip, which throws the results into separate .gz files. – Joe Sewell Jan 27 '15 at 17:58
  • tar -tf UNCID_2193585.70c7f658-5208-4b3f-9767-27a3b06b8ddc.120409_UNC14-SN744_0226_AC0M8NACXX_4_ACTTGA.tar.gz 120409_UNC14-SN744_0226_AC0M8NACXX_ACTTGA_L004_2.fastq 120409_UNC14-SN744_0226_AC0M8NACXX_ACTTGA_L004_1.fastq – Ron Jan 27 '15 at 18:54
  • For example The above shows one of the directories and it gives the name of the two files,now I should redirect this --to--stdout by piping? and pipe again then to gzip it ? – Ron Jan 27 '15 at 18:56

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