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#!/usr/bin/env perl -w
use TFBS::PatternGen::MEME;
use Test;
plan(tests => 5);
my $memepath;
eval {$memepath = `which meme 2> /dev/null`;};
if (!$memepath or ($memepath =~ / /)) { # if space, then error message :)
print "ok # Skipped: (no meme executable found)\n"x5;
exit(0);
}
my $fastafile = "t/test_meme.fa";
for (1..1) {
my $patterngen=TFBS::PatternGen::MEME->new(-seq_file=>$fastafile,
-additional_params=>' -revcomp -nmotifs 2 -w 10',
);
my @motifs=$patterngen->all_motifs;
if (@motifs>0){
ok(1);
my @sites=$motifs[0]->get_sites;
# my $seq=$sites[0]->seq->seq;
ok(1,($sites[0]->seq->seq ne ''));
}
my @pfms = $patterngen->all_patterns();
if (@pfms>0) {
ok(1);
ok(1,($pfms[0]->tag("score")>0));
last;
}
}
ok(1);
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