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  • osha84
    Junior Member
    • May 2013
    • 7

    #1

    awk search and replace

    Hi guys,

    I'm kinda new to shell scripting and I wrote this command in awk to go through on file line-by-line and search for "chr3,chr7,chr10,chr11,chr14,and chr20" in the first column and replace them all with "ch1" and the input file is tab delimited.

    I get an output file that is space delimited and it doesn't change all the variables to ch1, only the chr3 and chr7 will be changed to ch1 but chr10, chr11, and chr14 will be ch10 ch11 and ch14. the r is gone as I wanted but the numbers are still there.

    my code is

    Code:
    awk '{ gsub(/chr[3|7|10|11|14|17|20]/, "ch1", $1); print }' inFile > outFile
    Does anyone know what's wrong with my code?

    Thank you
  • osha84
    Junior Member
    • May 2013
    • 7

    #2
    I fixed the code,

    Thank you anyways

    Comment

    • GenoMax
      Senior Member
      • Feb 2008
      • 7142

      #3
      Originally posted by osha84 View Post
      I fixed the code,

      Thank you anyways
      Please post the fixed code so someone else coming along (via a search) is not left guessing what the fix was.

      Comment

      • osha84
        Junior Member
        • May 2013
        • 7

        #4
        I basically used the parentheses () in stead of using brackets []. That fixed the replacing issue and replaced all the chrs.

        my code after fixing it looks like this.
        Code:
        awk 'BEGIN {OFS="\t"} { gsub(/chr(3|7|10|11|14|17|20)/, "chr1", $1); print }' inFile > outFile

        Comment

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