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  • Adding counting Contig number at the start of Fasta Sequences

    I am trying to add Prefix to a list of Fasta sequences (30K+ which I have de-novo assembled) in a fasta file at the same time.

    I know from the past that have been able to add it at the end of the sequences. But I am getting a bit confused on how should I do it for the start of the Fasta sequence.

    For the end of sequence.
    Code:
    awk '/^>/{$0=$0"_Contig_"(++i)}1' input_file.fasta > output_file.fasta
    This will change something like this in the fasta file:

    From:
    >Sequence_header
    ATAGCATA
    To:
    >Sequences_header_Contig_1
    ATAGCATA
    ...
    >Sequences_header_Contig_n
    ATAGCATA


    I hope to do something like this:

    >Sequence_header
    ATAGCATA
    To:
    >Contig_1_Sequences_header
    ATAGCATA
    ...
    >Contig_n_Sequences_header
    ATAGCATA


    Code:
    awk '/^>/{"Contig_"(++i)"_"$0=$0}1' input_file.fasta > output_file.fasta
    Unfortunately I receive a synthax error.

    If someone could kindly show what I am doing wrong. I would greatly appreciate it.

    Many thanks.
    Last edited by Zapages; 05-09-2015, 05:02 PM.

  • #2
    Sorry, I don't speak awk.
    Code:
    perl -pe 'next unless /^>/; $i++; s/>(\S+)/>Contig_${i}_$1/' input_file.fasta > output_file.fasta
    seems to work.

    --
    Phillip

    Comment


    • #3
      How about this?

      Code:
      $  awk '{if (/^>/) print ">Contig_"(++i)"_" substr($0,2); else print $0;}'  your_file > new_file

      Comment


      • #4
        Thank you Phillip and Genomax. Both of the strategies work.

        Really appreciate all the help.

        Many Thanks,

        Zapages

        Comment

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