Why not represent your data in the way you wish to present it? create a 2-dimensional array using the line number of the file as your index when reading in the data.

subroutine{

    my @data;
    my $table;

    open( F, "$File" )
      || die("Could not open $File");
    
    while (<F>) {
        chomp();
        push( @{@data[$.]},( split /,/, $line));
    }
    close(F);

    $table .= "<table border=1>";

    for my $i ( 0 .. $#data ) {
        $table .= "<tr>";
        for ( @{@data[$i]}){
            $table .= "<td>$_</td>\r\n";
        }
        $table .= "</tr>";
    }
    $table .= "</table>";
}
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