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  • rename mutiple fasta header for mutiple fasta files

    Hi,

    I have mutiple fasta file and I want to change the header, for this I am using -

    awk '/^>/{print ">C1_" ++i; next}{print}' C1_pandaseq.fasta > C1_pandaseq_new.fasta

    input fasta-
    >M03419:60:656544:1:1101:25150:3877:1
    CCTACGGGTGGCTGCAGTGGGGAATTTTGGACAA
    >M03419:60:656544:1:1101:8498:4267:1
    ACTACGGGAGGCAGCAGGGGGGAATTTTGGACAATGGAAACCAGGG
    >M03419:60:656544:1:1101:7884:4445:1
    CCTACGGGTGGCAGCAGTGGGGAATATTGGACAATGCAACCCTGATCCAGC

    output fasta-
    >C1_1
    CCTACGGGTGGCTGCAGTGGGGAATTTTGGACAAAAAAAAAAAAAAAA
    >C1_2
    ACTACGGGAGGCAGCAGGGGGGAATTTTGGACAATGGAAACCAGGG
    >C1_3
    CCTACGGGTGGCAGCAGTGGGGAATATTGGACAATGCAACCCTGATCCAGC


    Similarly i have mutiple fasta file, which looks like-
    C2_pandaseq.fasta
    C4_pandaseq.fasta
    C5_pandaseq.fasta
    C8_pandaseq.fasta
    T2_pandaseq.fasta
    T7_pandaseq.fasta

    So I need to rename all the fasta file header, e.g.,

    for fasta file C2_pandaseq.fasta
    >C2_1
    AAAAAAAAAAAAAAAAAAAAAAA
    >C2_2
    ATTTTGGGGGGGGCCCCCCCGGGGGGGA


    for fasta file C4_pandaseq.fasta
    >C4_1
    AAAAAAAAAAAAAAAAAAAAAAA
    >C4_2
    ATTTTGGGGGGGGCCCCCCCGGGGGGGA


    and so on...

    For each fasta file, i need to rename fasta header according to the file name only. Therefore, I need to write a for loop for this, but i dont know how can i do that.

    Any help.
    Thanks

  • #2
    I would try something like:
    Code:
    for file in *_pandaseq.fasta
    do
    newname=$(echo $file |  sed s/_pandaseq.fasta//)
    awk '/^>/{print $newname ++i; next}{print}' $file > ${newname}_pandaseq_new.fasta
    done

    Comment


    • #3
      Originally posted by wdecoster View Post
      I would try something like:
      Code:
      for file in *_pandaseq.fasta
      do
      newname=$(echo $file |  sed s/_pandaseq.fasta//)
      awk '/^>/{print $newname ++i; next}{print}' $file > ${newname}_pandaseq_new.fasta
      done
      I have tried above for loop, but its not working.


      The output I got looks like -

      0
      CCTACGGGTGGCTGCAGTGGGGAATTTTGG
      0
      ACTACGGGAGGCAGCAGGGGGGAATTTTGGACA

      Comment

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