Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

        Latest Articles

        Collapse

        • seqadmin
          Exploring the Dynamics of the Tumor Microenvironment
          by seqadmin




          The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
          07-08-2024, 03:19 PM
        • seqadmin
          Exploring Human Diversity Through Large-Scale Omics
          by seqadmin


          In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
          06-25-2024, 06:43 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:53 AM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-10-2024, 07:30 AM
        0 responses
        34 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-03-2024, 09:45 AM
        0 responses
        204 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-03-2024, 08:54 AM
        0 responses
        213 views
        0 likes
        Last Post seqadmin  
        Working...
        X