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#!/usr/bin/env perl -w
use TFBS::PatternGen::Elph;
use TFBS::PatternGen::SimplePFM;
use Test;
plan(tests => 5);
my $gibbspath;
eval {$gibbspath = `which elph 2> /dev/null`;};
if (!$gibbspath or ($gibbspath =~ / /)) { # if space, then error message :)
print "ok # Skipped: (no elph executable found)\n"x5;
exit(0);
}
my $fastafile = "t/test_meme.fa";
#my $fastafile = $ARGV[0];
for (1..5) {
my $elph =
TFBS::PatternGen::Elph->new
(-motif_length=>7,
-seq_file=>$fastafile,
-additional_params=>'-l -x -b -g -v'
);
# print Dumper $elph;
my $pfm_elph = $elph->pattern();
my @pfms=$elph->all_patterns;
my @motifs=$elph->all_motifs;
if (@motifs>0){
ok(1);
my @sites=$motifs[0]->get_sites;
ok(1,($sites[0]->seq->seq ne ''));
my @matrix;
foreach my $site(@sites){
push @matrix,$site->seq->seq;
}
my $patt=TFBS::PatternGen::SimplePFM->new(-seq_list=>\@matrix);
my $col_sum=$elph->pattern->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("MAP_score")>0));
last;
}
}
ok(1);
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