From a5d1c9d86ab4ea41be8ecce10031d979d38fdd10 Mon Sep 17 00:00:00 2001
From: Laura Clarke <lec@sanger.ac.uk>
Date: Mon, 15 Apr 2002 13:12:50 +0000
Subject: [PATCH] added tests for GeneAdaptor and AnalysisAdaptor and removed
 print statements from gene.t

---
 modules/t/analysis.t | 55 +++++++++++++++++++++++++++++
 modules/t/clone.t    | 82 ++++++++++++++++++++++++++++++++++++++++++++
 modules/t/gene.t     |  6 ++--
 3 files changed, 140 insertions(+), 3 deletions(-)
 create mode 100644 modules/t/analysis.t
 create mode 100644 modules/t/clone.t

diff --git a/modules/t/analysis.t b/modules/t/analysis.t
new file mode 100644
index 0000000000..c1b2c621e7
--- /dev/null
+++ b/modules/t/analysis.t
@@ -0,0 +1,55 @@
+use lib 't';
+
+BEGIN { $| = 1;  
+	use Test;
+	plan tests => 7;
+}
+
+my $loaded = 0;
+END {print "not ok 1\n" unless $loaded;}
+
+use EnsTestDB;
+use Bio::EnsEMBL::DBLoader;
+
+
+
+$loaded = 1;
+
+ok(1);
+
+# Database will be dropped when this
+# object goes out of scope
+my $ens_test = EnsTestDB->new;
+
+$ens_test->do_sql_file("t/minidatabase.dump");
+my $db = $ens_test->get_DBSQL_Obj;
+ok($ens_test);
+
+my $analysis_ad = $db->get_AnalysisAdaptor();
+
+ok($analysis_ad);
+
+
+
+my $analysis = Bio::EnsEMBL::Analysis->new();
+
+$analysis->logic_name('dummy_analysis');
+$analysis->db('dummy');
+$analysis->program('dummy');
+$analysis->gff_source('dummy');
+$analysis->gff_feature('dummy');
+
+
+ok($analysis);
+
+$analysis_ad->store($analysis);
+
+
+ok(1);
+
+
+my $analysis_out = $analysis_ad->fetch_by_newest_logic_name('dummy_analysis');
+
+
+ok($analysis_out);
+ok($analysis_out->db eq 'dummy');
diff --git a/modules/t/clone.t b/modules/t/clone.t
new file mode 100644
index 0000000000..ec01cd7d04
--- /dev/null
+++ b/modules/t/clone.t
@@ -0,0 +1,82 @@
+use lib 't';
+
+BEGIN { $| = 1;  
+	use Test;
+	plan tests => 8;
+}
+
+my $loaded = 0;
+END {print "not ok 1\n" unless $loaded;}
+
+use EnsTestDB;
+use Bio::EnsEMBL::DBLoader;
+use Bio::EnsEMBL::PerlDB::Clone;
+use Bio::EnsEMBL::PerlDB::Contig;
+
+
+
+$loaded = 1;
+
+ok(1);
+
+# Database will be dropped when this
+# object goes out of scope
+my $ens_test = EnsTestDB->new;
+
+$ens_test->do_sql_file("t/minidatabase.dump");
+
+ok($ens_test);
+
+
+
+my $db = $ens_test->get_DBSQL_Obj;
+
+$clone_ad = $db->get_CloneAdaptor();
+
+
+my $clone = Bio::EnsEMBL::PerlDB::Clone->new();
+
+$clone->id('dummy_clone');
+$clone->embl_id('dummy_clone');
+$clone->embl_version(1);
+$clone->version(1);
+$clone->htg_phase(3);
+
+
+ok($clone);
+
+my $seq  = Bio::Seq->new(-seq => 'ATGCAGCTAGCATCGATGACATCG',
+		         -id => 'dummy_contig',
+	              	 -accession => 'dummy_contig');
+
+
+ok($seq);
+
+
+
+my $contig = Bio::EnsEMBL::PerlDB::Contig->new();
+
+
+
+$contig->id("dummy_contig");
+$contig->seq($seq);
+$contig->order(1);
+$contig->embl_offset(0);
+$contig->international_name("dummy_contig");
+
+$clone->add_Contig($contig);
+
+print STDERR "CONTIG ".$contig->primary_seq()."\n";
+ok($contig);
+
+
+$clone_ad->store($clone);
+
+ok(1);
+
+
+my $clone_out = $clone_ad->fetch_by_name('dummy_clone');
+
+ok($clone_out);
+
+ok($clone_out->embl_version == 1);
diff --git a/modules/t/gene.t b/modules/t/gene.t
index ce11650d21..5f858ea036 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -149,7 +149,7 @@ my @exons = $gene_out->get_all_Exons();
 
 @sorted_exons = sort{$a->start <=> $b->start}@exons;
 
-print STDERR "EXON 1 START = ".$sorted_exons[0]->start."\n";
+
 
 ok($sorted_exons[0]->start==5);
 
@@ -166,9 +166,9 @@ ok($sorted_exons[2]->phase==0);
 my $pep;
 my $translate = 0;
 foreach my $trans($gene->each_Transcript()){
-	print STDERR $trans->seq->seq."\n";
+	
 	my $pep = $trans->translate();
-	print STDERR "PEP ".$pep->seq()."\n";
+
 	if($pep !=~ /\*/){
 	    $translate = 1;
         }else{
-- 
GitLab