/usr/share/doc/libtfbs-perl/examples/t/09_Word_Consensus.t is in libtfbs-perl 0.7.0+dfsg-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #!/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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