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  • convert a text file in fasta with decollpasing

    Hi all,

    I have this file:

    TGAGGTAGTAGATTGTATAGTT 424866
    TAGCTTATCAGACTGATGTTGA 359141
    TAGCTTATCAGACTGATGTTGAC 276052
    TGAGGTAGTAGGTTGTATAGTT 268735
    ACAGTAGTCTGCACATTGGTT 209280
    ACAGTAGTCTGCACATTGGTTA 178652
    TAGCTTATCAGACTGATGTTG 166159
    TGAGGTAGTAGGTTGTGTGGTT 105275
    TGAGGTAGTAGGTTGTATGGTT 102447
    AGCAGCATTGTACAGGGCTATGA 91296
    TGAGGTAGTAGGTTGTGTGGTTT 63300
    TGAGGTAGTAGTTTGTACAGTT 61604
    TGAGGTAGTAGATTGTATAGT 61492
    TAGCACCATCTGAAATCGGTTA 60637
    TTCAAGTAATCCAGGATAGGCT 52300
    TGAGGTAGTAGATTGTATAGTTA 50905
    TGAGGTAGTAGGTTGTATAGT 48150
    TACAGTAGTCTGCACATTGGTT 47534
    TCTACAGTCCGACGATC 45803
    ................

    They are sequences and the numbers are the respective occurrences. I would like to convert that file in a fasta format, decollapsing the sequences and giving a name like that:

    >Sample1_0
    TGAGGTAGTAGATTGTATAGTT
    >Sample1_1
    TGAGGTAGTAGATTGTATAGTT
    >Sample1_2
    TGAGGTAGTAGATTGTATAGTT
    .....
    for 424866 times.
    >Sample1_424666
    TGAGGTAGTAGATTGTATAGTT

    then
    >Sample1_424667
    TAGCTTATCAGACTGATGTTGA (the second sequences)

    The same for the other sequences in series. Is there any scripts for that purpose?

    Thanks in advance,
    Giorgio

  • #2
    Code:
    awk '{for(i=0;i<=($2-1);i++) print ">Sample"NR"_"i"\n"$1}' file.txt
    This might work!

    Comment


    • #3
      Thanks vivek it works great!

      Comment


      • #4
        This can also be done with Biopieces (www.biopieces.org):

        Code:
        read_tab -i in.tab -k SEQ,COUNT | duplicate_record -k COUNT | add_ident -k SEQ_NAME -p Sample1_ | write_fasta -x

        Comment

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