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  • Perl Help

    Hi All,

    When I upload the junction.bed file to UCSC, there was an error happen: "the chromosome name is case sensitive..." because name of chromosome is "1, 2, 3, 4,..." in my bowtie index.

    I wanted to change the name "1, 2, 3..." to "chr1, chr2, chr3...", then I use this code "perl -pi -e 's/^/chr/' filename" But I met an issue, since I run this code two times by accident , then the first string of each line of bed file became this embarrassing condition: "chrchr1,chrchr2,chrchr3..."

    Does anyone can help me to change it back to chr1.....? I am not familiar with Perl.

    Many thanks in advance!

  • #2
    perl -ane 's/chrchr/chr/g; print;' filename

    Comment


    • #3
      Thank you very much, RockChalkJayhawk, that works very well.

      Comment


      • #4
        Sorry, I am sort of silly at that time. I can just use text editor and then replace all.

        Comment


        • #5
          Originally posted by RockChalkJayhawk View Post
          perl -ane 's/chrchr/chr/g; print;' filename
          Or,

          perl -pe 's/chrchr/chr/g'

          accomplishes the same thing. -a isn't used in this context. and -p is like -n but prints every line.

          If your fingers are tired, might make a difference...

          --
          Phillip

          Comment


          • #6
            Originally posted by pmiguel View Post
            Or,

            perl -pe 's/chrchr/chr/g'

            accomplishes the same thing. -a isn't used in this context. and -p is like -n but prints every line.

            If your fingers are tired, might make a difference...

            --
            Phillip
            You can learn something new everyday. Thanks Phillip!

            Comment


            • #7
              Thanks RockChalkJayhawk and Phillip!

              Comment


              • #8
                Your original line probably should have been

                perl -pi -e 's/^([^c])/chr$1/'

                Comment


                • #9
                  Thanks Keith

                  Originally posted by krobison View Post
                  Your original line probably should have been

                  perl -pi -e 's/^([^c])/chr$1/'

                  Was just wondering.

                  Comment


                  • #10
                    Originally posted by krobison View Post
                    Your original line probably should have been

                    perl -pi -e 's/^([^c])/chr$1/'
                    or create a back up file in case the in place edit (-i) goes awry:

                    perl -i'.bak' -pe 's/^/chr/' file.bed

                    because if you find out you hosed file.bed, you can

                    mv file.bed.bak file.bed

                    to recover.

                    --
                    Phillip

                    Comment

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