I used Parallel::ForkManager to scan the motifs in DNA string pairs. The script is the following:

my $multi_cpu_num      = 13;
my @ciona_pwm_array    = getCionaPWM();
my $output_temp        = 'temp.ciona.temp';
my $output_temp_handle = FileHandle->new(">output_temp");
my $output_handle      = FileHandle->new(">ciona.matrix.result");
my $result_buffer      = undef;
foreach my $id (1..100) {
    my $seq_1 = 'gatctatcgtagcagcta';
    my $seq_2 = 'agtctacatgctacgatg';
    my $pm    = Parallel::ForkManager->new( $multi_cpu_num );
    PWM:
    for my $pwm (@ciona_pwm_array) {
        $pm->start and next PWM;
        my $count = count_pwm_num($pwm,$seq_1,$seq_2);
        if($count != 0) {
            $output_temp_handle->print($id);
            $output_temp_handle->print("\t$pwm\t1\n");
        }
        else {
            $output_temp_handle->print($id);
            $output_temp_handle->print("\t$pwm\t0\n");
        }
        $pm->finish;
    }
    $pm->wait_all_children;
}

$output_temp_handle->close;

# catch the Parallel::ForkManager output
# the temporary output looks like that
# a A 1
# b B 0
# c C 1
# a B 1
# in real code , I used 1, 2,3, instead of a, b, c ,d.

my $reopen_handle = FileHandle->new($output_temp);
while(my $line = $reopen_handle->getline) {
      chomp $line;
      my @buffer = split/\t/,$line;
      $result_buffer->{$buffer[0]}->{$buffer[1]} = $buffer[2];
}

$reopen_handle->close;
unlink 'temp.ciona.temp';

# print output_header_information :row 1 in program result table;
$output_handle->print("id");
foreach my $pwm (@ciona_pwm_array) {
      $output_handle->print("\t$pwm");
}
$output_handle->print("\n");

# print the content of program result table

foreach my $id (1..100}) {
    $output_handle->print("$id");
    foreach my $pwm (@ciona_pwm_array) {
          my $count = $result_buffer->{$id}->{$pwm};
          $output_handle->print("\t$count");
    }
    $output_handle->print("\n");
}


$output_handle->close;

sub ciona_pwm_num {}
sub getCionaPWM {]

exit(0);
[download]

There are three parameters for the function count_pwm_num. The first one is $pwm, which is from list @ciona_pwm_array and is the motif feature. The second and third are DNA strings. The function is to calculate the motif number (how many?)using motif feature $pwm in the DNA strings. The aim of the function count_pwm_num is to report the motif number from both strings. The following table is the report from the program. However, I calculated the same DNA strings 100 times ( the first for-loop) and used same motif list (@ciona_pwm_array, the second for-loop), there is always missed motif(s) in the report. For example, row a (first row), the program reported all six motif number from A-F. row b missed the number of the motif A (because they were same DNA strings, the output should keep the same). row c missed the number of motif B.row d missed the number for motif A and B. It seemed the missed motif numbers were randomly selected. So my question is: why count_pwm_num randomly skip some $pwm and do not perform the function of count_pwm_num?

program result table:

id	A	B	C	D	E	F
a	1	1	0	1	1	0
b		1	0	1	1	0
c	1		0	1	1	0
d			0	1	1	0
e	1	1	0	1	1	0
..

Expected result

id	A	B	C	D	E	F
a	1	1	0	1	1	0
b	1	1	0	1	1	0
c	1	1	0	1	1	0
d	1	1	0	1	1	0
e	1	1	0	1	1	0
..

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