[Bioperl-guts-l] bioperl commit

Heikki Lehvaslaiho heikki at pub.open-bio.org
Tue Mar 9 06:33:26 EST 2004


heikki
Tue Mar  9 06:33:26 EST 2004
Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv18896

Modified Files:
	sirna.t 
Log Message:
fuller use of the Test module and bioperl conventions

bioperl-live/t sirna.t,1.3,1.4
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/sirna.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/bioperl/bioperl-live/t/sirna.t	2004/03/09 02:51:11	1.3
+++ /home/repository/bioperl/bioperl-live/t/sirna.t	2004/03/09 11:33:26	1.4
@@ -1,64 +1,62 @@
+# This is -*-Perl-*- code
+## Bioperl Test Harness Script for Modules
+##
+## $Id$
+
+use strict;
+use vars qw($NUMTESTS $DEBUG $ERROR);
+$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
+BEGIN {
+    # to handle systems with no installed Test module
+    # we include the t dir (where a copy of Test.pm is located)
+    # as a fallback
+    eval { require Test; };
+    $ERROR = 0;
+    if( $@ ) {
+	use lib 't';
+    }
+    use Test;
 
-use Test;
-
-BEGIN { plan tests => 4 };
+    $NUMTESTS = 7;
+    plan tests => $NUMTESTS;
+}
 
 use Bio::Tools::SiRNA;
 use Bio::Seq;
 use Bio::SeqIO;
 
+
 # modules compile
-print "ok 1\n";
+ok 1;
 
 my $input = Bio::SeqIO->new( -file 	=> 't/data/NM_002254.gb',
 			     -format 	=> 'Genbank' );
-
 my $seq = $input->next_seq;
 
-my $sirna = Bio::Tools::SiRNA->new( -target 	=> $seq,
-				    );
+#object creation
+ok my $sirna = Bio::Tools::SiRNA->new( -target 	=> $seq,
+                                     );
 
 # first test - cds only
- my @pairs = $sirna->design;
-
- print "CDS only: got ",scalar(@pairs),"\n";
-
- if( scalar(@pairs) == 65 ) {
-     print "ok 2\n";
- } else {
-     print "not ok 2\n";
- }
-
+my @pairs = $sirna->design;
+ok scalar(@pairs), 65, "CDS only: got ". scalar(@pairs) ;
 
 
 # next test - include 3prime utr
 my @feats = $seq->remove_SeqFeatures;
-
 foreach my $feat (@feats) {
-    $seq->add_SeqFeature($feat) unless 
+    $seq->add_SeqFeature($feat) unless
 	($feat->primary_tag eq 'Target' or $feat->isa('Bio::SeqFeature::SiRNA::Pair'));
 }
-$sirna->include_3pr(1);
-
- at pairs2 = $sirna->design;
- print "With 3p UTR: got ",scalar(@pairs2),"\n";
+ok $sirna->include_3pr(1);
+ at pairs = $sirna->design;
+print "With 3p UTR: got ",scalar(@pairs),"\n" if $DEBUG;
+ok  scalar(@pairs), 140;
 
-if( scalar(@pairs2) == 140 ) {
-    print "ok 3\n";
-} else {
-    print "not ok 3\n";
-}
 
 #third test - naked sequence
 my $newseq = Bio::Seq->new( -seq => $seq->seq);
-
-$sirna->target($newseq);
-
- at pairs3 = $sirna->design;
- print "Bare sequence: got ",scalar(@pairs3),"\n";
-
-if( scalar(@pairs3) == 142 ) {
-    print "ok 4\n";
-} else {
-    print "not ok 4\n";
-}
+ok $sirna->target($newseq);
+ at pairs = $sirna->design;
+print "Bare sequence: got ",scalar(@pairs),"\n" if $DEBUG;
+ok scalar(@pairs),  142;



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