extract characters between two commas?





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1















I have a file with ~ 3 million rows, here is the first few lines of my file:



head out.txt
NA
NA
NA
NA
NA
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753,gene85754
gene85752,gene85753,gene85754
gene85752,gene85753,gene85754
gene85752,gene85753,gene85754
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752,gene85753
gene85752
gene85752


For those rows that are separated by ",", I want to keep everything after the first comma and before the second comma.
This is my desired output:



outgood.txt
NA
NA
NA
NA
NA
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85753
gene85752
gene85752









share|improve this question





























    1















    I have a file with ~ 3 million rows, here is the first few lines of my file:



    head out.txt
    NA
    NA
    NA
    NA
    NA
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753,gene85754
    gene85752,gene85753,gene85754
    gene85752,gene85753,gene85754
    gene85752,gene85753,gene85754
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752,gene85753
    gene85752
    gene85752


    For those rows that are separated by ",", I want to keep everything after the first comma and before the second comma.
    This is my desired output:



    outgood.txt
    NA
    NA
    NA
    NA
    NA
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85753
    gene85752
    gene85752









    share|improve this question

























      1












      1








      1








      I have a file with ~ 3 million rows, here is the first few lines of my file:



      head out.txt
      NA
      NA
      NA
      NA
      NA
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753,gene85754
      gene85752,gene85753,gene85754
      gene85752,gene85753,gene85754
      gene85752,gene85753,gene85754
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752
      gene85752


      For those rows that are separated by ",", I want to keep everything after the first comma and before the second comma.
      This is my desired output:



      outgood.txt
      NA
      NA
      NA
      NA
      NA
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85752
      gene85752









      share|improve this question














      I have a file with ~ 3 million rows, here is the first few lines of my file:



      head out.txt
      NA
      NA
      NA
      NA
      NA
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753,gene85754
      gene85752,gene85753,gene85754
      gene85752,gene85753,gene85754
      gene85752,gene85753,gene85754
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752,gene85753
      gene85752
      gene85752


      For those rows that are separated by ",", I want to keep everything after the first comma and before the second comma.
      This is my desired output:



      outgood.txt
      NA
      NA
      NA
      NA
      NA
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85753
      gene85752
      gene85752






      text-processing awk






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked 2 hours ago









      Anna1364Anna1364

      439213




      439213






















          3 Answers
          3






          active

          oldest

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          3














          Since cut prints non-delimited lines by default the following works



          cut -f2 -d, file





          share|improve this answer



















          • 1





            It's nice when someone remember the little quirks of standard tools.

            – Kusalananda
            1 hour ago



















          1














          awk -F, 'NF > 1 { $1 = $2 } { print $1 }' file


          This uses awk to parse the file as lines consisting of comma-delimited fields.



          The code detects when there is more than a single field on a line, and when there is, the first field is replaced by the second field. The first field, either unmodified or modified by the conditional code, is then printed.






          share|improve this answer































            0














            awk -F, 'NF == 1 {print $1}
            NF > 1 { print $2}' filename


            This will print just the first string if there is no comma, second string if there is one or more comma.






            share|improve this answer
























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              3 Answers
              3






              active

              oldest

              votes








              3 Answers
              3






              active

              oldest

              votes









              active

              oldest

              votes






              active

              oldest

              votes









              3














              Since cut prints non-delimited lines by default the following works



              cut -f2 -d, file





              share|improve this answer



















              • 1





                It's nice when someone remember the little quirks of standard tools.

                – Kusalananda
                1 hour ago
















              3














              Since cut prints non-delimited lines by default the following works



              cut -f2 -d, file





              share|improve this answer



















              • 1





                It's nice when someone remember the little quirks of standard tools.

                – Kusalananda
                1 hour ago














              3












              3








              3







              Since cut prints non-delimited lines by default the following works



              cut -f2 -d, file





              share|improve this answer













              Since cut prints non-delimited lines by default the following works



              cut -f2 -d, file






              share|improve this answer












              share|improve this answer



              share|improve this answer










              answered 1 hour ago









              iruvariruvar

              12.3k63062




              12.3k63062








              • 1





                It's nice when someone remember the little quirks of standard tools.

                – Kusalananda
                1 hour ago














              • 1





                It's nice when someone remember the little quirks of standard tools.

                – Kusalananda
                1 hour ago








              1




              1





              It's nice when someone remember the little quirks of standard tools.

              – Kusalananda
              1 hour ago





              It's nice when someone remember the little quirks of standard tools.

              – Kusalananda
              1 hour ago













              1














              awk -F, 'NF > 1 { $1 = $2 } { print $1 }' file


              This uses awk to parse the file as lines consisting of comma-delimited fields.



              The code detects when there is more than a single field on a line, and when there is, the first field is replaced by the second field. The first field, either unmodified or modified by the conditional code, is then printed.






              share|improve this answer




























                1














                awk -F, 'NF > 1 { $1 = $2 } { print $1 }' file


                This uses awk to parse the file as lines consisting of comma-delimited fields.



                The code detects when there is more than a single field on a line, and when there is, the first field is replaced by the second field. The first field, either unmodified or modified by the conditional code, is then printed.






                share|improve this answer


























                  1












                  1








                  1







                  awk -F, 'NF > 1 { $1 = $2 } { print $1 }' file


                  This uses awk to parse the file as lines consisting of comma-delimited fields.



                  The code detects when there is more than a single field on a line, and when there is, the first field is replaced by the second field. The first field, either unmodified or modified by the conditional code, is then printed.






                  share|improve this answer













                  awk -F, 'NF > 1 { $1 = $2 } { print $1 }' file


                  This uses awk to parse the file as lines consisting of comma-delimited fields.



                  The code detects when there is more than a single field on a line, and when there is, the first field is replaced by the second field. The first field, either unmodified or modified by the conditional code, is then printed.







                  share|improve this answer












                  share|improve this answer



                  share|improve this answer










                  answered 1 hour ago









                  KusalanandaKusalananda

                  140k17261435




                  140k17261435























                      0














                      awk -F, 'NF == 1 {print $1}
                      NF > 1 { print $2}' filename


                      This will print just the first string if there is no comma, second string if there is one or more comma.






                      share|improve this answer




























                        0














                        awk -F, 'NF == 1 {print $1}
                        NF > 1 { print $2}' filename


                        This will print just the first string if there is no comma, second string if there is one or more comma.






                        share|improve this answer


























                          0












                          0








                          0







                          awk -F, 'NF == 1 {print $1}
                          NF > 1 { print $2}' filename


                          This will print just the first string if there is no comma, second string if there is one or more comma.






                          share|improve this answer













                          awk -F, 'NF == 1 {print $1}
                          NF > 1 { print $2}' filename


                          This will print just the first string if there is no comma, second string if there is one or more comma.







                          share|improve this answer












                          share|improve this answer



                          share|improve this answer










                          answered 1 hour ago









                          unxnutunxnut

                          3,79721120




                          3,79721120






























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