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#!/usr/bin/env perl -w
use TFBS::Matrix::PFM;
use strict;
use Test;
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 $siteset = $pfm->to_PWM->search_seq(-file=>'t/test.fa',-threshold=>"70%");
ok($siteset->size(), 20);
print $siteset->GFF();
my $sitepairset =
$pfm->to_PWM->search_aln(-file=>'t/test.aln',
-window=>50, -cutoff=>50,
-threshold=>"70%");
my $It = $sitepairset->Iterator();
my $startsum = 0;
while (my $sitepair = $It->next) {
$startsum += $sitepair->feature1->start;
}
ok($startsum, 3013);
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