Dear monks,

I've written perl codes below. My wish that this code should give output : how many times each motif match with the sequences ($dna), but $regexp (variable contain multiple motifs) only read the last motif instead of 11 motifs (in subroutine its give 11 motifs, but when I call the function its give only 1 motif). Please help me what's wrong with my scripts. Thanks in advance.

use strict;
use warnings;

my @file_data = ();
my %motif_hash = ();
my $dna;
my $regexp;
my @positions = (); 
my $site;
my @motifs;
my $match;
my $count;

@file_data = get_file_data("promoters.txt");
$dna = extract_sequence(@file_data);
$regexp = parseMOTIF('motifs.txt');
print "Regexp: '$regexp'\n";


$match = match_positions($count);
push(@positions,$match);
print "match : $match";

sub match_positions{
    my($regexp,$dna) = @_;
    my $count= 0;
    my @positions;
    my $regexp;
    my $dna;
    while ($dna =~ /$regexp/g){
        push(@positions,pos($dna)-length($&)+1);
        ++$count;
        }
        return $count;
}

sub parseMOTIF {
    use strict;
    use warnings;
    my @motiffile = ();
    my $name;
    my $site;
    my $regexp;
    my %motif_hash = ();
    my $motiffile = $_[0];


    @motiffile = get_file_data($motiffile);

    foreach $motiffile(@motiffile){
        if($motiffile =~ /(^[A|S]\d+\s+|^[A|S]\d+b\s+)([A-Z]+)(\s+.*)$
+/){
        my $name = $1;
        my $site = $2;
        $regexp = IUB_to_regexp($site);
        $motif_hash{$name} = "$site $regexp\n";
        print "motif : $site\n";
        print "The regexp : $regexp\n";
        }     
           }    
           return $regexp;

}

sub get_file_data{
    my ($filename)=@_;
    use strict;
    use warnings;
    my @filedata=();
    
    unless(open(GET_FILE_DATA, $filename)){
        print STDERR "can't open file $filename\"\n\n";
        exit;
    }
    
    @filedata = <GET_FILE_DATA>;
    close GET_FILE_DATA;
    return @filedata;
}

sub extract_sequence {
     use strict;
     my (@file_data) = @_;
     use warnings;
     my $sequence = "";
     foreach my $line(@file_data) {
     if ($line =~ /^>/){
     next;
     }
     else {
     $sequence .= $line; 
     }
    }
    #$sequence =~ s/\s//g;
    return $sequence;
}

sub IUB_to_regexp{
    my($iub) = @_;
    my $regular_expression ="";
    my %iub2char_class = (
                A =>'A',   
                C =>'C',
                G =>'G',
                T =>'T',
                R =>'GA',
                Y =>'CT',
                M =>'AC',
                K =>'GT',
                S =>'GC',
                W =>'AT',
                B =>'CGT',
                D =>'AGT',
                H =>'ACT',
                V =>'ACG',
                N =>'ACGT',
                );

    for (my $i=0;$i<length($iub);$i++){
    $regular_expression .= $iub2char_class{substr($iub,$i,1)};
    }
    return $regular_expression;
}
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