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  • How to combine all the seqences in a fasta file to one sequence?

    Hi every one,

    I have a fasta file like this like this:
    >GL132456
    ABCDEDERFSE
    >GL123456
    ABDFDRAGDTGEGAGFDAS
    >GL125436
    AFGHSRSGFGSHSFG
    I want to combine all the sequences to one sequence, like this:
    ABCDEDERFSEABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG

    Thanks a lot!

    Richard

  • #2
    Maybe:

    Code:
    grep -v ">" your.fasta | sed -e 's/\n//g' -e 's/ //g' > youredited.fasta
    Select all lines than don't have ">", remove newlines, remove spaces, direct output to a new file.
    Last edited by rhinoceros; 10-26-2013, 06:03 PM.
    savetherhino.org

    Comment


    • #3
      Originally posted by rhinoceros View Post
      Maybe:

      Code:
      grep -v ">" your.fasta | sed -e 's/\n//g' -e 's/ //g' > youredited.fasta
      Select all lines than don't begin with ">", remove newlines, remove spaces, direct output to a new file.
      Just a minor update of above would create the required output:

      Code:
      grep -v ">" your.fasta|tr '\n' ' ' | sed -e 's/ //g' > youredited.fasta
      Output:

      ABCDEDERFSEABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG

      Comment


      • #4
        use cat command

        Comment


        • #5
          I have checked all the commands. No one worked for my data.
          Thanks!

          Comment


          • #6
            Originally posted by wmseq View Post
            I have checked all the commands. No one worked for my data.
            Thanks!
            You're doing it wrong then because they do work:

            Code:
            $ cat file.fasta 
            >GL132456
            ABCDEDERFSE
            >GL123456
            ABDFDRAGDTGEGAGFDAS
            >GL125436
            AFGHSRSGFGSHSFG
            
            $ grep -v ">" file.fasta | tr '\n' ' ' | sed -e 's/ //g' > youredited.fasta
            
            $ cat youredited.fasta 
            ABCDEDERFSEABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG
            savetherhino.org

            Comment


            • #7
              I am sorry for my mistake, because my sequence is as follows.
              >GL132456
              ABCDEDERFSE
              DGA
              >GL123456
              ABDFDRAGDTGEGAGFDAS
              >GL125436
              AFGHSRSGFGSHSFG

              After I used the commands, I got the following sequence with white space in it.
              ABCDEDERFSE
              DGA
              ABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG

              thank you for your patience!
              Last edited by wmseq; 10-28-2013, 07:05 AM.

              Comment


              • #8
                perl -pe 'chomp;s/>.+//' input.fasta >out.txt

                Comment

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