#!/freeware/bin/perl -W

use Bio::SeqIO;
use Bio::Tools::GFF;

my $seqFile = $ARGV[0];
my $gffFile = $ARGV[1];

my $gffio = new Bio::Tools::GFF(-file => "<$gffFile", 
               -gff_version => 2);

my $seqio = new Bio::SeqIO( -file => "<$seqFile",
                -format => 'fasta');


# first get length of sequences
my $L = 0;
my $C = 0;
while ( my $seq = $seqio->next_seq() ){
    $L += $seq->length;
    $C++;
    #print STDERR $seq->id,": ",$seq->length,"\n";
}
$seqio->close;

my %list = ();
my %motifs = ();
my $cc = 0;
while ( my $gff = $gffio->next_feature() ){

    # motif ID
    my $id = 'dummy';
    if ( $gff->has_tag('id') ){
    $id = join '', $gff->each_tag_value('id');
    }
    #print STDERR "\r",$cc++;

    if ( defined $list{$id} ){
    $list{$id}++;
    }else{
    $list{$id} = 1;
    my $site = '';
    if ( $gff->has_tag('site') ){
        $site = join '', $gff->each_tag_value('site');
    }
    $motifs{$id} = length($site);
    }
}
#print STDERR "\n";


foreach my $k ( keys %list ){
    my $value = $list{$k}/ ( 2*($L - ($C * ($motifs{$k} - 1))));
    print $k,"\t",$value,"\n";
}

$gffio->close;