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  • Split long fasta seq into smaller seqs by removing 'n'

    Hello,

    My fasta file has a long consensus sequence (gigabases long) that is padded with 'n' between the actual sequences. Like this:

    actgggacnnnnnnnnnnnnnnnnnnnnnnnnnnactgacgtggattgc
    aatnnnnnnnnnnnnnnnaccaattggatagagaccnnn

    I've searched rather intensively to see if the internet can solve my problem. Not really, though they were close. For example, people report splitting the long sequence into smaller files but I do not want that. I want the n removed and have all sequences in the same file. Better yet, with the start and end of the sequences.

    Desired output (>seqname_start_end) :
    >seq1_1_8
    actgggac

    >seq2_35_52
    actgacgtggattgcaat

    >seq3_68_85
    accaattggatagagacc

    If anyone could point me towards a right tool (bioperl, etc) or give me a pseudo-code in perl, I would appreciate it.

    Thanks.

  • #2
    IDBA contains a script called split_scaffold

    Contribute to loneknightpy/idba development by creating an account on GitHub.


    Here's what it does:

    IN =>

    >test
    acgacgacgacgacgacgacgacagcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacgacgacgacagcagtagatgatgatagtag


    OUT =>

    >teste_0
    ACGACGACGACGACGACGACGACAGCA
    >teste_1
    ACGACGACGACAGCAGTAGATGATGATAGTAG

    Comment


    • #3
      Originally posted by azneto View Post
      IDBA contains a script called split_scaffold

      Contribute to loneknightpy/idba development by creating an account on GitHub.

      Great! Thanks a lot! Worked flawlessly.

      It doesn't get me the start/end of the base positions but that I can live with.

      Comment

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