Cleaning a genes database polluted by non-numeric characters except plus and minus signs

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I have this genes database which is completely messed up by extra non-alphanumeric values. This happened as a sort of encryption to the data which was made incorrectly, and I don't know how to clean it up. I tried sed and awk, but failed. This is sample of the data which is a very large amount of documents:



chr2#@!!~//=^%$74711&&*&127472363@Pos1%%0^^+
chr3#@!!~//=^%$74723&&*&127473530@Pos2%%0^^+
chr1#@!!~//=^%$73530&&*&127474697@Pos3%%0^^+
chr2#@!!~//=^%$17469&&*&127475864@Pos4%%0^^+
chr3#@!!~//=^%$12747&&*&127477031@Neg1%%0^^-
chr5#@!!~//=^%$17477&&*&127478198@Neg2%%0^^-
chr7#@!!~//=^%$74781&&*&127479365@Neg3%%0^^-
chr7#@!!~//=^%$74795&&*&127480532@Pos5%%0^^+
chr1#@!!~//=^%$12748&&*&127481699@Neg4%%0^^-


The cleaned data must be like this:



chr2 74711 127472363 Pos1 0 +
chr3 74723 127473530 Pos2 0 +
chr1 73530 127474697 Pos3 0 +
chr2 17469 127475864 Pos4 0 +
chr3 12747 127477031 Neg1 0 -
chr5 17477 127478198 Neg2 0 -
chr7 74781 127479365 Neg3 0 -
chr7 74795 127480532 Pos5 0 +
chr1 12748 127481699 Neg4 0 -


How can I do this?






text-processing awk sed bioinformatics







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  • try sed -E 's/[^a-zA-Z0-9+-]+/ /g' file
    – mosvy
    20 hours ago






  • 1




    What have your tried? I don't see any code showing effort to solve the problem.
    – Pedro Lobito
    12 hours ago














up vote
3
down vote

favorite












I have this genes database which is completely messed up by extra non-alphanumeric values. This happened as a sort of encryption to the data which was made incorrectly, and I don't know how to clean it up. I tried sed and awk, but failed. This is sample of the data which is a very large amount of documents:



chr2#@!!~//=^%$74711&&*&127472363@Pos1%%0^^+
chr3#@!!~//=^%$74723&&*&127473530@Pos2%%0^^+
chr1#@!!~//=^%$73530&&*&127474697@Pos3%%0^^+
chr2#@!!~//=^%$17469&&*&127475864@Pos4%%0^^+
chr3#@!!~//=^%$12747&&*&127477031@Neg1%%0^^-
chr5#@!!~//=^%$17477&&*&127478198@Neg2%%0^^-
chr7#@!!~//=^%$74781&&*&127479365@Neg3%%0^^-
chr7#@!!~//=^%$74795&&*&127480532@Pos5%%0^^+
chr1#@!!~//=^%$12748&&*&127481699@Neg4%%0^^-


The cleaned data must be like this:



chr2 74711 127472363 Pos1 0 +
chr3 74723 127473530 Pos2 0 +
chr1 73530 127474697 Pos3 0 +
chr2 17469 127475864 Pos4 0 +
chr3 12747 127477031 Neg1 0 -
chr5 17477 127478198 Neg2 0 -
chr7 74781 127479365 Neg3 0 -
chr7 74795 127480532 Pos5 0 +
chr1 12748 127481699 Neg4 0 -


How can I do this?






text-processing awk sed bioinformatics







share|improve this question









New contributor




marco is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.



















  • try sed -E 's/[^a-zA-Z0-9+-]+/ /g' file
    – mosvy
    20 hours ago






  • 1




    What have your tried? I don't see any code showing effort to solve the problem.
    – Pedro Lobito
    12 hours ago












up vote
3
down vote

favorite









up vote
3
down vote

favorite











I have this genes database which is completely messed up by extra non-alphanumeric values. This happened as a sort of encryption to the data which was made incorrectly, and I don't know how to clean it up. I tried sed and awk, but failed. This is sample of the data which is a very large amount of documents:



chr2#@!!~//=^%$74711&&*&127472363@Pos1%%0^^+
chr3#@!!~//=^%$74723&&*&127473530@Pos2%%0^^+
chr1#@!!~//=^%$73530&&*&127474697@Pos3%%0^^+
chr2#@!!~//=^%$17469&&*&127475864@Pos4%%0^^+
chr3#@!!~//=^%$12747&&*&127477031@Neg1%%0^^-
chr5#@!!~//=^%$17477&&*&127478198@Neg2%%0^^-
chr7#@!!~//=^%$74781&&*&127479365@Neg3%%0^^-
chr7#@!!~//=^%$74795&&*&127480532@Pos5%%0^^+
chr1#@!!~//=^%$12748&&*&127481699@Neg4%%0^^-


The cleaned data must be like this:



chr2 74711 127472363 Pos1 0 +
chr3 74723 127473530 Pos2 0 +
chr1 73530 127474697 Pos3 0 +
chr2 17469 127475864 Pos4 0 +
chr3 12747 127477031 Neg1 0 -
chr5 17477 127478198 Neg2 0 -
chr7 74781 127479365 Neg3 0 -
chr7 74795 127480532 Pos5 0 +
chr1 12748 127481699 Neg4 0 -


How can I do this?






text-processing awk sed bioinformatics







share|improve this question









New contributor




marco is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











I have this genes database which is completely messed up by extra non-alphanumeric values. This happened as a sort of encryption to the data which was made incorrectly, and I don't know how to clean it up. I tried sed and awk, but failed. This is sample of the data which is a very large amount of documents:



chr2#@!!~//=^%$74711&&*&127472363@Pos1%%0^^+
chr3#@!!~//=^%$74723&&*&127473530@Pos2%%0^^+
chr1#@!!~//=^%$73530&&*&127474697@Pos3%%0^^+
chr2#@!!~//=^%$17469&&*&127475864@Pos4%%0^^+
chr3#@!!~//=^%$12747&&*&127477031@Neg1%%0^^-
chr5#@!!~//=^%$17477&&*&127478198@Neg2%%0^^-
chr7#@!!~//=^%$74781&&*&127479365@Neg3%%0^^-
chr7#@!!~//=^%$74795&&*&127480532@Pos5%%0^^+
chr1#@!!~//=^%$12748&&*&127481699@Neg4%%0^^-


The cleaned data must be like this:



chr2 74711 127472363 Pos1 0 +
chr3 74723 127473530 Pos2 0 +
chr1 73530 127474697 Pos3 0 +
chr2 17469 127475864 Pos4 0 +
chr3 12747 127477031 Neg1 0 -
chr5 17477 127478198 Neg2 0 -
chr7 74781 127479365 Neg3 0 -
chr7 74795 127480532 Pos5 0 +
chr1 12748 127481699 Neg4 0 -


How can I do this?






text-processing awk sed bioinformatics




text-processing awk sed bioinformatics






share|improve this question









New contributor




marco is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











share|improve this question









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edited 20 mins ago









Peter Mortensen

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asked 21 hours ago









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  • try sed -E 's/[^a-zA-Z0-9+-]+/ /g' file
    – mosvy
    20 hours ago






  • 1




    What have your tried? I don't see any code showing effort to solve the problem.
    – Pedro Lobito
    12 hours ago
















  • try sed -E 's/[^a-zA-Z0-9+-]+/ /g' file
    – mosvy
    20 hours ago






  • 1




    What have your tried? I don't see any code showing effort to solve the problem.
    – Pedro Lobito
    12 hours ago















try sed -E 's/[^a-zA-Z0-9+-]+/ /g' file
– mosvy
20 hours ago




try sed -E 's/[^a-zA-Z0-9+-]+/ /g' file
– mosvy
20 hours ago




1




1




What have your tried? I don't see any code showing effort to solve the problem.
– Pedro Lobito
12 hours ago




What have your tried? I don't see any code showing effort to solve the problem.
– Pedro Lobito
12 hours ago










3 Answers
3






active

oldest

votes

















up vote
12
down vote



accepted










You can do it with sed. Something as follows:



sed 's/[^a-zA-Z0-9+-]/ /g' file | column -tc2

chr2 74711 127472363 Pos1 0 +
chr3 74723 127473530 Pos2 0 +
chr1 73530 127474697 Pos3 0 +
chr2 17469 127475864 Pos4 0 +
chr3 12747 127477031 Neg1 0 -
chr5 17477 127478198 Neg2 0 -
chr7 74781 127479365 Neg3 0 -
chr7 74795 127480532 Pos5 0 +
chr1 12748 127481699 Neg4 0 -





share|improve this answer
















  • 1




    THIS IS AMAZING!!!!!!!!!!!!! thank you @goro i didn't know how to keep - and +
    – marco
    20 hours ago






  • 1




    Proving answers to users who didn't show any effort to solve the problem isn't encouraged.
    – Pedro Lobito
    12 hours ago






  • 2




    @PedroLobito Says who? This isn't a teaching website, it's a website dedicated to collect answers to problems.
    – pipe
    10 hours ago










  • Says the SO community rules.
    – Pedro Lobito
    2 hours ago

















up vote
8
down vote













With tr, transliterating characters from the complement of the wanted set to spaces, and squeezing repeats:



$ tr -sc '[:alnum:][:space:]+-' ' ' < data
chr2 74711 127472363 Pos1 0 +
chr3 74723 127473530 Pos2 0 +
chr1 73530 127474697 Pos3 0 +
chr2 17469 127475864 Pos4 0 +
chr3 12747 127477031 Neg1 0 -
chr5 17477 127478198 Neg2 0 -
chr7 74781 127479365 Neg3 0 -
chr7 74795 127480532 Pos5 0 +
chr1 12748 127481699 Neg4 0 -





share|improve this answer





























    up vote
    0
    down vote













    An awk solution



    awk -F '[^[:alnum:]+-]+' '$1=$1;print' file





    share|improve this answer




















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      3 Answers
      3






      active

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      3 Answers
      3






      active

      oldest

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      active

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      up vote
      12
      down vote



      accepted










      You can do it with sed. Something as follows:



      sed 's/[^a-zA-Z0-9+-]/ /g' file | column -tc2

      chr2 74711 127472363 Pos1 0 +
      chr3 74723 127473530 Pos2 0 +
      chr1 73530 127474697 Pos3 0 +
      chr2 17469 127475864 Pos4 0 +
      chr3 12747 127477031 Neg1 0 -
      chr5 17477 127478198 Neg2 0 -
      chr7 74781 127479365 Neg3 0 -
      chr7 74795 127480532 Pos5 0 +
      chr1 12748 127481699 Neg4 0 -





      share|improve this answer
















      • 1




        THIS IS AMAZING!!!!!!!!!!!!! thank you @goro i didn't know how to keep - and +
        – marco
        20 hours ago






      • 1




        Proving answers to users who didn't show any effort to solve the problem isn't encouraged.
        – Pedro Lobito
        12 hours ago






      • 2




        @PedroLobito Says who? This isn't a teaching website, it's a website dedicated to collect answers to problems.
        – pipe
        10 hours ago










      • Says the SO community rules.
        – Pedro Lobito
        2 hours ago














      up vote
      12
      down vote



      accepted










      You can do it with sed. Something as follows:



      sed 's/[^a-zA-Z0-9+-]/ /g' file | column -tc2

      chr2 74711 127472363 Pos1 0 +
      chr3 74723 127473530 Pos2 0 +
      chr1 73530 127474697 Pos3 0 +
      chr2 17469 127475864 Pos4 0 +
      chr3 12747 127477031 Neg1 0 -
      chr5 17477 127478198 Neg2 0 -
      chr7 74781 127479365 Neg3 0 -
      chr7 74795 127480532 Pos5 0 +
      chr1 12748 127481699 Neg4 0 -





      share|improve this answer
















      • 1




        THIS IS AMAZING!!!!!!!!!!!!! thank you @goro i didn't know how to keep - and +
        – marco
        20 hours ago






      • 1




        Proving answers to users who didn't show any effort to solve the problem isn't encouraged.
        – Pedro Lobito
        12 hours ago






      • 2




        @PedroLobito Says who? This isn't a teaching website, it's a website dedicated to collect answers to problems.
        – pipe
        10 hours ago










      • Says the SO community rules.
        – Pedro Lobito
        2 hours ago












      up vote
      12
      down vote



      accepted







      up vote
      12
      down vote



      accepted






      You can do it with sed. Something as follows:



      sed 's/[^a-zA-Z0-9+-]/ /g' file | column -tc2

      chr2 74711 127472363 Pos1 0 +
      chr3 74723 127473530 Pos2 0 +
      chr1 73530 127474697 Pos3 0 +
      chr2 17469 127475864 Pos4 0 +
      chr3 12747 127477031 Neg1 0 -
      chr5 17477 127478198 Neg2 0 -
      chr7 74781 127479365 Neg3 0 -
      chr7 74795 127480532 Pos5 0 +
      chr1 12748 127481699 Neg4 0 -





      share|improve this answer












      You can do it with sed. Something as follows:



      sed 's/[^a-zA-Z0-9+-]/ /g' file | column -tc2

      chr2 74711 127472363 Pos1 0 +
      chr3 74723 127473530 Pos2 0 +
      chr1 73530 127474697 Pos3 0 +
      chr2 17469 127475864 Pos4 0 +
      chr3 12747 127477031 Neg1 0 -
      chr5 17477 127478198 Neg2 0 -
      chr7 74781 127479365 Neg3 0 -
      chr7 74795 127480532 Pos5 0 +
      chr1 12748 127481699 Neg4 0 -






      share|improve this answer












      share|improve this answer



      share|improve this answer










      answered 21 hours ago









      Goro

      7,19253168




      7,19253168







      • 1




        THIS IS AMAZING!!!!!!!!!!!!! thank you @goro i didn't know how to keep - and +
        – marco
        20 hours ago






      • 1




        Proving answers to users who didn't show any effort to solve the problem isn't encouraged.
        – Pedro Lobito
        12 hours ago






      • 2




        @PedroLobito Says who? This isn't a teaching website, it's a website dedicated to collect answers to problems.
        – pipe
        10 hours ago










      • Says the SO community rules.
        – Pedro Lobito
        2 hours ago












      • 1




        THIS IS AMAZING!!!!!!!!!!!!! thank you @goro i didn't know how to keep - and +
        – marco
        20 hours ago






      • 1




        Proving answers to users who didn't show any effort to solve the problem isn't encouraged.
        – Pedro Lobito
        12 hours ago






      • 2




        @PedroLobito Says who? This isn't a teaching website, it's a website dedicated to collect answers to problems.
        – pipe
        10 hours ago










      • Says the SO community rules.
        – Pedro Lobito
        2 hours ago







      1




      1




      THIS IS AMAZING!!!!!!!!!!!!! thank you @goro i didn't know how to keep - and +
      – marco
      20 hours ago




      THIS IS AMAZING!!!!!!!!!!!!! thank you @goro i didn't know how to keep - and +
      – marco
      20 hours ago




      1




      1




      Proving answers to users who didn't show any effort to solve the problem isn't encouraged.
      – Pedro Lobito
      12 hours ago




      Proving answers to users who didn't show any effort to solve the problem isn't encouraged.
      – Pedro Lobito
      12 hours ago




      2




      2




      @PedroLobito Says who? This isn't a teaching website, it's a website dedicated to collect answers to problems.
      – pipe
      10 hours ago




      @PedroLobito Says who? This isn't a teaching website, it's a website dedicated to collect answers to problems.
      – pipe
      10 hours ago












      Says the SO community rules.
      – Pedro Lobito
      2 hours ago




      Says the SO community rules.
      – Pedro Lobito
      2 hours ago












      up vote
      8
      down vote













      With tr, transliterating characters from the complement of the wanted set to spaces, and squeezing repeats:



      $ tr -sc '[:alnum:][:space:]+-' ' ' < data
      chr2 74711 127472363 Pos1 0 +
      chr3 74723 127473530 Pos2 0 +
      chr1 73530 127474697 Pos3 0 +
      chr2 17469 127475864 Pos4 0 +
      chr3 12747 127477031 Neg1 0 -
      chr5 17477 127478198 Neg2 0 -
      chr7 74781 127479365 Neg3 0 -
      chr7 74795 127480532 Pos5 0 +
      chr1 12748 127481699 Neg4 0 -





      share|improve this answer


























        up vote
        8
        down vote













        With tr, transliterating characters from the complement of the wanted set to spaces, and squeezing repeats:



        $ tr -sc '[:alnum:][:space:]+-' ' ' < data
        chr2 74711 127472363 Pos1 0 +
        chr3 74723 127473530 Pos2 0 +
        chr1 73530 127474697 Pos3 0 +
        chr2 17469 127475864 Pos4 0 +
        chr3 12747 127477031 Neg1 0 -
        chr5 17477 127478198 Neg2 0 -
        chr7 74781 127479365 Neg3 0 -
        chr7 74795 127480532 Pos5 0 +
        chr1 12748 127481699 Neg4 0 -





        share|improve this answer
























          up vote
          8
          down vote










          up vote
          8
          down vote









          With tr, transliterating characters from the complement of the wanted set to spaces, and squeezing repeats:



          $ tr -sc '[:alnum:][:space:]+-' ' ' < data
          chr2 74711 127472363 Pos1 0 +
          chr3 74723 127473530 Pos2 0 +
          chr1 73530 127474697 Pos3 0 +
          chr2 17469 127475864 Pos4 0 +
          chr3 12747 127477031 Neg1 0 -
          chr5 17477 127478198 Neg2 0 -
          chr7 74781 127479365 Neg3 0 -
          chr7 74795 127480532 Pos5 0 +
          chr1 12748 127481699 Neg4 0 -





          share|improve this answer














          With tr, transliterating characters from the complement of the wanted set to spaces, and squeezing repeats:



          $ tr -sc '[:alnum:][:space:]+-' ' ' < data
          chr2 74711 127472363 Pos1 0 +
          chr3 74723 127473530 Pos2 0 +
          chr1 73530 127474697 Pos3 0 +
          chr2 17469 127475864 Pos4 0 +
          chr3 12747 127477031 Neg1 0 -
          chr5 17477 127478198 Neg2 0 -
          chr7 74781 127479365 Neg3 0 -
          chr7 74795 127480532 Pos5 0 +
          chr1 12748 127481699 Neg4 0 -






          share|improve this answer














          share|improve this answer



          share|improve this answer








          edited 20 hours ago

























          answered 20 hours ago









          steeldriver

          32.6k34980




          32.6k34980




















              up vote
              0
              down vote













              An awk solution



              awk -F '[^[:alnum:]+-]+' '$1=$1;print' file





              share|improve this answer
























                up vote
                0
                down vote













                An awk solution



                awk -F '[^[:alnum:]+-]+' '$1=$1;print' file





                share|improve this answer






















                  up vote
                  0
                  down vote










                  up vote
                  0
                  down vote









                  An awk solution



                  awk -F '[^[:alnum:]+-]+' '$1=$1;print' file





                  share|improve this answer












                  An awk solution



                  awk -F '[^[:alnum:]+-]+' '$1=$1;print' file






                  share|improve this answer












                  share|improve this answer



                  share|improve this answer










                  answered 6 hours ago









                  iruvar

                  11.6k62959




                  11.6k62959




















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