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#!/usr/bin/env perl -w
use TFBS::PatternGen::AnnSpec;
use TFBS::PatternGen::SimplePFM;
use Test;
plan(tests => 7);
my $annspecpath;
eval {$annspecpath = `which ann-spec 2> /dev/null`;};
if (!$annspecpath or ($annspecpath =~ / /)) { # if space, then error message :)
print "ok # Skipped: (no AnnSpec executable found)\n"x7;
exit(0);
}
my $fastafile = "t/test_meme.fa";
#my $fastafile=$ARGV[0];
for (1..5) {
my $patterngen=TFBS::PatternGen::AnnSpec->new(-seq_file=>$fastafile,
#-binary=>'ann-spec',
-additional_params=>'-P 5 -c'
);
my @pfms = $patterngen->all_patterns();
my @motifs=$patterngen->all_motifs;
if (@motifs>0){
ok(1);
my @sites=$motifs[0]->get_sites;
ok(1,($sites[0]->seq->seq ne ''));
my @seqs;
foreach my $site(@sites){
push @seqs,$site->seq->seq;
}
print $pfms[0]->rawprint;
my $seq=$sites[0]->seq->seq;
my $patt=TFBS::PatternGen::SimplePFM->new(-seq_list=>\@seqs);
my $col_sum=$pfms[0]->matrix->[0]->[0];
my $check_sum=$patt->pattern->matrix->[0]->[0];
ok(1,$col_sum==$check_sum);
}
if (@pfms>0) {
ok(1);
ok(1,($pfms[0]->tag("score")>0));
last;
}
}
ok(1);
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