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use Test;
use TFBS::Ext::pwmsearch;
use TFBS::Matrix::PFM;
plan(tests=>2);
my $matrixstring =
"0 0 0 0 0 0 0 0\n".
"0 12 12 0 12 0 12 12\n".
"0 0 0 12 0 12 0 0\n".
"12 0 0 0 0 0 0 0";
my $pfm = TFBS::Matrix::PFM->new(-matrix=>$matrixstring,
-name=>"MyMatrix");
my $pwm = $pfm->to_PWM;
my $seq = Bio::SeqIO->new(-file=>"t/test.fa", -format=>"fasta")->next_seq();
my $siteset1 = TFBS::Ext::pwmsearch::pwmsearch($pwm, $seq, "60%");
my $siteset2 = TFBS::Ext::pwmsearch::pwmsearch($pwm, $seq, "60%");
ok($siteset1->size(), 194);
#print STDERR "SIZE::".$siteset1->size()."\n";
my $it = $siteset2->Iterator();
my $startsum = 0;
while (my $site = $it->next()) {
$startsum += $site->start;
}
#print STDERR "STARTSUM::".$startsum."\n";
ok($startsum, 457608);
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