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#!/usr/bin/env perl -w
use TFBS::Word::Consensus;
use Test;
plan(tests => 2);
# print STDERR join("\n", @INC);
my $word = "AGGTCMNNNNKGACCT";
my $word_obj = TFBS::Word::Consensus->new(-word=>$word,
-name=>"MyConsensus");
print $word_obj->to_PWM->prettyprint;
my $siteset = $word_obj->search_seq(-file=>'t/test.fa',
-threshold=>"70%",
-max_mismatches => 4);
ok($siteset->size(), 6);
#print $siteset->GFF."\n\n";
my $sitepairset =
$word_obj->search_aln(-file=>'t/test.aln',
-window=>50, -cutoff=>50,
-max_mismatches=>6);
#print $sitepairset->GFF;
my $It = $sitepairset->Iterator();
my $startsum = 0;
while (my $sitepair = $It->next) {
$startsum += $sitepair->feature1->start;
}
ok($sitepairset->size, 24);
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