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#!/usr/local/bin/perl
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 9);
use_ok('Bio::Tools::Run::Promoterwise');
use_ok('Bio::Seq');
}
my $verbose = -1;
my @params = ('-verbose' => test_debug(), 'silent' => 1, 'quiet' => 1);
my $factory = Bio::Tools::Run::Promoterwise->new(@params);
isa_ok $factory,'Bio::Tools::Run::Promoterwise';
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 6);
my $bequiet = 1;
$factory->quiet($bequiet); # Suppress pseudowise messages to terminal
#test with one file with 2 sequences
my $inputfilename = test_input_file('sim4_cdna.fa');
my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
-format => 'fasta');
my $seq1 = Bio::Seq->new();
$seq1 = $seqstream1->next_seq();
$inputfilename = test_input_file('sim4_genomic.fa');
my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
-format => 'fasta');
my $seq2 = Bio::Seq->new();
$seq2 = $seqstream2->next_seq();
my @fp = $factory->run($seq1, $seq2);
my $first = $fp[0]->feature1;
my $second = $fp[0]->feature2;
my @sub = $first->sub_SeqFeature;
my @sub2 = $second->sub_SeqFeature;
is $sub[0]->start,4;
is $sub2[0]->start,29;
is $sub[0]->end,18;
is $sub2[0]->end,43;
is $sub[0]->seq->seq,'GTTGTGCTGGGGGGG';
is $sub[0]->score,1596.49;
}
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