updated unit tests

Changes

@@ -152,7 +152,7 @@ Revision history for Perl extension Bio::ViennaNGS.
 	- added scripts/bed2nt2aa.pl
 	- updated POD and README
 
-0.17 Thu Jun 08 2017
+0.17 Fri Jun 09 2017
 	- added Bio::ViennaNGS::FeatureIO
 	- added Bio::ViennaNGS::Subtypes
 	- refactored Bio::ViennaNGS::Fasta to transparently coerce input

MANIFEST

@@ -62,7 +62,8 @@ share/template-TrackHub/description.html
 share/template-TrackHub/genome.txt
 share/template-TrackHub/hub.txt
 share/template-TrackHub/trackDb.txt
-t/01-basics.t
+t/00-prereq.t
+t/01-load.t
 t/02-thirdparty.t
 t/04-UCSC-TrackHub.t
 t/05-UCSC-AssemblyHub.t
@@ -71,3 +72,4 @@ t/07-FeatureIO.t
 t/08-FeatureInterval.t
 t/09-MinimalFeature.t
 t/10-Features.t
+t/11-BedGraphEntry.t

Makefile.PL

@@ -63,7 +63,9 @@ WriteMakefile(
 					      'ExtUtils::MakeMaker' => 0,
 					     },
 	      'BUILD_REQUIRES' => {
-				   'Test::More' => 0,
+				   "Test::More" => 0,
+				   'Test::Prereq' => 0,
+
 				  },
 	      dist  => { COMPRESS => 'gzip -9f', SUFFIX => 'gz', },
 	      clean => { FILES => 'Bio-ViennaNGS-*' },

t/01-load.t

@@ -0,0 +1,60 @@
+#-*-Perl-*-
+
+use strict;
+use warnings;
+use Test::More tests => 20;
+
+BEGIN {
+      use_ok('Bio::ViennaNGS') ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS\n";
+      use_ok('Bio::ViennaNGS::AnnoC')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::AnnoC\n";	
+      use_ok('Bio::ViennaNGS::Bam')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Bam\n";
+      use_ok('Bio::ViennaNGS::Bed')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Bed\n";
+      use_ok('Bio::ViennaNGS::BedGraphEntry')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::BedGraphEntry\n";
+      use_ok('Bio::ViennaNGS::Expression')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Expression\n";
+      use_ok('Bio::ViennaNGS::ExtFeature')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::ExtFeature\n";
+      use_ok('Bio::ViennaNGS::Fasta')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Fasta\n";
+      use_ok('Bio::ViennaNGS::Feature')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Feature\n";
+      use_ok('Bio::ViennaNGS::FeatureChain')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::FeatureChain\n";
+      use_ok('Bio::ViennaNGS::FeatureLine')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::FeatureLine\n";
+      use_ok('Bio::ViennaNGS::FeatureInterval')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Featureinterval\n";
+      use_ok('Bio::ViennaNGS::FeatureIO')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::FeatureIO\n";
+      use_ok('Bio::ViennaNGS::MinimalFeature')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::MinimalFeature\n";
+      use_ok('Bio::ViennaNGS::Peak')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Peak\n";
+      use_ok('Bio::ViennaNGS::SpliceJunc')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::SpliceJunc\n";
+      use_ok('Bio::ViennaNGS::Subtypes')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Subtypes\n";
+      use_ok('Bio::ViennaNGS::Tutorial')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::tutorial\n";
+      use_ok('Bio::ViennaNGS::UCSC')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::UCSC\n";
+      use_ok('Bio::ViennaNGS::Util')  ||  print "Bail out! Cannot load Bio::RNA::ViennaNGS::Util\n";
+}
+
+
+diag( "Test Bio::ViennaNGS $Bio::ViennaNGS::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::AnnoC $Bio::ViennaNGS::AnnoC::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Bam $Bio::ViennaNGS::Bam::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Bed $Bio::ViennaNGS::Bed::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::BedGraphEntry $Bio::ViennaNGS::BedGraphEntry::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Expression $Bio::ViennaNGS::Expression::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::ExtFeature $Bio::ViennaNGS::ExtFeature::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Fasta $Bio::ViennaNGS::Fasta::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Feature $Bio::ViennaNGS::Feature::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::FeatureChain $Bio::ViennaNGS::FeatureChain::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::FeatureLine $Bio::ViennaNGS::FeatureLine::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::FeatureInterval $Bio::ViennaNGS::FeatureInterval::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::FeatureIO $Bio::ViennaNGS::FeatureIO::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::MinimalFeature $Bio::ViennaNGS::MinimalFeature::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Peak $Bio::ViennaNGS::Peak::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::SpliceJunc $Bio::ViennaNGS::SpliceJunc::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Subtypes $Bio::ViennaNGS::Subtypes::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Tutorial $Bio::ViennaNGS::Tutorial::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::UCSC $Bio::ViennaNGS::UCSC::VERSION, Perl $], $^X" );
+diag( "Test Bio::ViennaNGS::Util $Bio::ViennaNGS::Util::VERSION, Perl $], $^X" );
+
+#ok( defined(can_run('cat')), 'cat not found');
+#ok( defined(can_run('awk')), 'awk not found');
+#ok( defined(can_run('bedToBigBed')), 'bedToBigBed not found'); 
+#ok( defined(can_run('genomeCoverageBed')), 'genomeCoverageBed not found');
+#ok( defined(can_run('bedGraphToBigWig')), 'bedGraphToBigWig not found');
+#ok( defined(can_run('faToTwoBit')), 'faToTwoBit not found');
+#ok( defined(can_run('bedtools')), 'bedtools not found');
+#ok( defined(can_run('sortBed')), 'sortBed not found');
+#########################

t/03-Fasta.t

@@ -16,7 +16,6 @@ BEGIN {
       use lib 't';
     }
     use Test::More tests => TEST_COUNT;
-    print Dumper($Bin);
 }
 
 use Bio::ViennaNGS::Fasta;

t/07-FeatureIO.t

@@ -17,7 +17,6 @@ BEGIN {
       use lib 't';
     }
     use Test::More tests => TEST_COUNT;
-    print Dumper($Bin);
 }
 
 use Bio::ViennaNGS::FeatureIO;

t/08-FeatureInterval.t

@@ -17,7 +17,6 @@ BEGIN {
       use lib 't';
     }
     use Test::More tests => TEST_COUNT;
-    print Dumper($Bin);
 }
 
 use Bio::ViennaNGS::FeatureInterval;

t/09-MinimalFeature.t

@@ -17,7 +17,6 @@ BEGIN {
       use lib 't';
     }
     use Test::More tests => TEST_COUNT;
-    print Dumper($Bin);
 }
 
 use Bio::ViennaNGS::MinimalFeature;

t/11-BedGraphEntry.t

@@ -0,0 +1,33 @@
+#-*-Perl-*-
+
+use strict;
+use warnings;
+use Path::Class;
+use File::Share ':all';
+use Data::Dumper;
+use FindBin qw($Bin);
+use constant TEST_COUNT => 2;
+
+use lib "$Bin/../lib", "$Bin/../blib/lib", "$Bin/../blib/arch";
+
+BEGIN {
+    # include Test.pm from 't' dir in case itis not installed
+    eval { require Test::More; };
+    if ($@) {
+      use lib 't';
+    }
+    use Test::More tests => TEST_COUNT;
+}
+
+use Bio::ViennaNGS::BedGraphEntry;
+
+{
+  my $chr = "chrX";
+  my $start = 99999;
+  my $end = 123456;
+  my $value = 234433.434354;
+  my @arg = (chromosome => $chr, start => $start, end => $end, dataValue => $value);
+  my $BGE = new_ok('Bio::ViennaNGS::BedGraphEntry'=> \@arg);
+  ok($BGE->_length == 23457, 'length of underlying Featureinterval');
+}
+