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  • Add count numbers to headers in a fasta file

    Hi all,

    I have a fasta file with the same header for each sequence, I would like to add natural numbers at the end of each line:

    >OakDna
    ACTCTAAATCAGTGCGAG...
    >OakDna
    AAAAACCCTTTACACTTT...
    >OakDna
    CTCTAAACCTTTAACCTT..
    etc.

    I want something like this:

    >OakDna_1
    ACTCTAAATCAGTGCGAG...
    >OakDna_2
    AAAAACCCTTTACACTTT...
    >OakDna_3
    CTCTAAACCTTTAACCTT..
    etc.
    >OakDna_n
    ACTCATCCAAAACTTTTT..

    Where n is the last number of the sequence in the file.

    Any quick suggestion?

    Thanks in advance,
    Giorgio

  • #2
    Google is your friend in situations like these:

    http://www.linuxquestions.org/questi...f-line-803625/

    Comment


    • #3
      I tried to google it, but couldn't find what I was looking for. Btw the link you posted seems to be good...THANKS a lot!

      Comment


      • #4
        I'd just write a simple program to do it

        5 min ?

        Comment


        • #5
          Here a quick and dirty solution in python - was still missing :-)


          #!/usr/bin/env python

          import re
          import string
          import sys


          infile = open(sys.argv[1])
          data = infile.readlines()
          infile.close()

          outfile = open(sys.argv[2], "w")
          c = 1
          l = 1
          for i in data:
          i = re.sub("\n|\r", "", i)
          if c%2 != 0:
          outfile.write(i+"_" +str(l) +"\n")
          l+=1
          else:
          outfile.write(i +"\n")
          c += 1
          outfile.close()


          save the upper code in a file called for example "numberFasta.py"
          on a terminal call the program with: python numberFasta.py <yourInfile> <outfilename>

          Comment


          • #6
            ah..and correct the indention - was lost here...

            Comment


            • #7
              Originally posted by wieni View Post
              Here a quick and dirty solution in python - was still missing :-)


              #!/usr/bin/env python

              import re
              import string
              import sys


              infile = open(sys.argv[1])
              data = infile.readlines()
              infile.close()

              outfile = open(sys.argv[2], "w")
              c = 1
              l = 1
              for i in data:
              i = re.sub("\n|\r", "", i)
              if c%2 != 0:
              outfile.write(i+"_" +str(l) +"\n")
              l+=1
              else:
              outfile.write(i +"\n")
              c += 1
              outfile.close()


              save the upper code in a file called for example "numberFasta.py"
              on a terminal call the program with: python numberFasta.py <yourInfile> <outfilename>
              You can use the "code" tags to make this work (surround the code with [code ] and [/code ] (but no spaces):

              Code:
              #!/usr/bin/env python
              
              import re
              import string
              import sys
              
              
              infile = open(sys.argv[1])
              data = infile.readlines()
              infile.close()
              
              outfile = open(sys.argv[2], "w")
              c = 1
              l = 1
              for i in data:
                  i = re.sub("\n|\r", "", i)
                  if c%2 != 0:
                      outfile.write(i+"_" +str(l) +"\n")
                      l+=1
                  else:
                      outfile.write(i +"\n")
                  c += 1
              outfile.close()

              Comment


              • #8
                A short one:

                Code:
                awk '/^>/{$0=$0"_"(++i)}1' infile

                Comment

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