Well, I had to do something similar to this recently. This is the code that i used to read my input from a file into an array or arrays, aka a matrix. This was the subroutine to put it into a matrix, which other subs then moved about, ultimately putting into another file. Hope it helps some.

        open FILE, "<input.txt";
    open OUTP, ">output.txt";
    undef (@matrix);
    while (<FILE>){
    push @matrix, [split];
    }
    &dataconvert; # this is where it branched off to 
                  #change up the data
    select OUTP;
        for $i (0.. ($#matrix)){
    print "@{$matrix[$i]} \n";
    }
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It simply pushed the contents of the file into a matrix using push. I hope this helps you out a bit.