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  • concatenating fasta files with TAB seperating loci

    Hi,

    I have a problem concatenating files so that I can load them into Arlequin. I have a few thousand fasta (or nexus) files each representing a single gene. However, not all individuals are present in all files. I want to concatenate these in such a way, that missing genes are filled with Ns or ? or - and that genes are seperated by TAB. I have found many tools, but none allowed TAB seperation of loci. I would be happy for any ideas.

    Examples:

    Input 1
    Neo001_0 CGTAAAAATTTGTTCCGAAACATA
    Neo001_1 CGTAAAAATTTGTTCCGAAACATA
    Neo003_0 CGTAAAAATTTGTTCCGAAACATA
    Neo003_1 CGTAAAAATTTGTTCCGAAACATA
    Neo004_0 CGTAAAAATTTGTTCCGAAACATA
    Neo004_1 CGTAAAAATTTGTTCCGAAACATA


    Input2
    Neo001_0 CGATGTATTTGGTATCCTAC
    Neo001_1 CGATGTATTTGGTATCCTAC
    Neo002_0 CGATGTATTTGGTATCCTAC
    Neo002_1 CGATGTATTTGGTATCCTAC
    Neo003_0 CGATGTATTTGGTATCCTAC
    Neo003_1 CGATGTATTTGGTATCCTAC
    Neo004_0 CGATGTATTTGGTATCCTAC
    Neo004_1 CGATGTATTTGGTATCCTAC




    Expected output:
    Expected output:
    Neo001_0 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
    Neo001_1 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
    Neo002_0 NNNNNNNNNNNNNNNNNNNNNNNN CGATGTATTTGGTATCCTAC
    Neo002_1 NNNNNNNNNNNNNNNNNNNNNNNN CGATGTATTTGGTATCCTAC
    Neo003_0 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
    Neo003_1 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
    Neo004_0 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
    Neo004_1 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC


    Many thanks,
    Martin

  • #2
    The concatenate function of Seqkit [https://bioinf.shenwei.me/seqkit/usage/#concat] will concatenate sequences with matching ID's from two fasta files.

    I converted your inputs into fasta format and the following command concatenated matching ID's together.

    $seqkit concat input1.txt input2.txt >output.txt

    But it did not add the N's and there is no space delimiting the two sequences. Maybe you can get it to add a delimiter.

    Comment


    • #3
      Sometimes the old solutions are the best solutions, the good ol' Unix join command:

      Code:
      join -e 'NNNNNNNNNNNNNNNNNNNNNNNN' -1 1 -2 1 -a 1 -a 2 -o '0,1.2,2.2' Input1.txt Input2.txt
      Assumptions
      • Your input files as shown are named Input1.txt and Input2.txt
      • The input files have both been sorted prior to running the join command


      Read the man page for join to learn what all the various command line parameters are doing.

      Comment

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