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  • bash shell question

    I tried to do a simple task in batch--unzipping many gz files. I have many .gz files, but how come it only unzipped one file then finished? Anything wrong with my script? thanks. John


    ## unzip fastq.gz
    for i in *.fastq.gz
    do
    #echo $i
    zcat "$i" > "${i%.*}"
    done

  • #2
    have you tried 'gunzip *.fastq.gz' ?

    Comment


    • #3
      gunzip *.fastq.gz will delete original gz files. i want to keep original files.



      Originally posted by azneto View Post
      have you tried 'gunzip *.fastq.gz' ?

      Comment


      • #4
        for i in `ls *.fastq.gz`; do gunzip -c $i > $i.fastq; done

        Comment


        • #5
          I tried
          for i in `ls *.fastq.gz`; do gunzip -c $i > ${i%.gz}; done

          still only unzipped just first file then finished. no error. very strange.


          Originally posted by azneto View Post
          for i in `ls *.fastq.gz`; do gunzip -c $i > $i.fastq; done

          Comment


          • #6
            I tested your version of the command and it worked fine. It could be something related to permissions.

            Comment


            • #7
              thanks. I thought it might be related to something internal. will find out.

              Originally posted by azneto View Post
              I tested your version of the command and it worked fine. It could be something related to permissions.

              Comment


              • #8
                for i in $(ls *.gz); do sn=`echo $i | sed 's/\.gz$//'`; zcat $i > $sn; done;

                Comment


                • #9
                  another nice way to do it.

                  I really think something is going on with my server. It still finished after doing one file. I will ask my admin tomorrow. Will let you know.

                  By any chance did this happen to any one of you here?

                  Originally posted by Richard Finney View Post
                  for i in $(ls *.gz); do sn=`echo $i | sed 's/\.gz$//'`; zcat $i > $sn; done;

                  Comment

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