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  • The format of the ooc file in Blat

    Hi, I'm new here.

    Blat produces ooc file to store the over-repetitive fragment in the chromosomes. I wonder whether the format specification of this ooc file is public, or there is any program to parse it.

    Thanks a lot.

  • #2
    I wrote a PERL script to decode it.
    The sequence database is a subset of hg19, including
    chr1 to chr22, chrX, chrY, and chrM.

    The tileSize I used is 11.

    There are 30031 11-mer excluded in the ooc file.

    The decoded file looks like:
    1480676850
    11
    0
    1
    2
    3
    4
    5
    6
    8
    9
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    20
    21
    22
    24
    25
    26
    27
    32
    33
    34
    .....
    4193279
    4193535
    4194046
    4194047
    4194303

    Here is the code:
    $in="11.ooc";
    open(IN, "< $in");
    binmode(IN);
    open(OUT, "> out");
    while (read(IN,$b,4)) {
    $byteCount++;
    $a=unpack("V",$b);
    print(OUT $a."\n");
    }

    Comment


    • #3
      this is great, thank you.

      Comment

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