1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
|
#!/usr/bin/env perl -w
use TFBS::PatternGen::Gibbs;
use Test;
plan(tests => 5);
my $gibbspath;
eval {$gibbspath = `which Gibbs 2> /dev/null`;};
if (!$gibbspath or ($gibbspath =~ / /)) { # if space, then error message :)
print "ok # Skipped: (no Gibbs executable found)\n"x5;
exit(0);
}
my $fastafile = "t/test.gibbin";
for (1..5) {
my $gibbs =
TFBS::PatternGen::Gibbs->new
(-nr_hits=>10,
-motif_length=>[10..12],
-seq_file=>$fastafile);
my @pfms = $gibbs->all_patterns();
my @motifs=$gibbs->all_motifs;
if (@motifs>0){
ok(1);
my @sites=$motifs[0]->get_sites;
# my $seq=$sites[0]->seq->seq;
ok(1,($sites[0]->seq->seq ne ''));
}
if (@pfms>0) {
ok(1);
ok(1,($pfms[0]->tag("MAP_score")>0));
last;
}
}
ok(1);
|
