From 607efca23d862aa068f664fa93a8db9436a5bde2 Mon Sep 17 00:00:00 2001
From: Nathan Johnson <njohnson@ebi.ac.uk>
Date: Fri, 3 Jun 2011 14:16:30 +0000
Subject: [PATCH] added BaseFeatureAdaptor fetch_Iterator tests
---
modules/t/iterator.t | 60 ++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 58 insertions(+), 2 deletions(-)
diff --git a/modules/t/iterator.t b/modules/t/iterator.t
index 36b1e56a11..7cab29ff1d 100644
--- a/modules/t/iterator.t
+++ b/modules/t/iterator.t
@@ -3,8 +3,9 @@ use warnings;
use Test::More;
use Data::Dumper;
+$|=1;
-BEGIN {
+BEGIN {
use_ok('Bio::EnsEMBL::Utils::Iterator');
}
@@ -127,5 +128,60 @@ $num = 0;
Bio::EnsEMBL::Utils::Iterator->new([1..12])->each(sub { $num++; });
is($num, 12, 'each iterates over all elements');
-done_testing;
+
+
+# test BaseFeatureAdaptor Iterator methods
+
+use Bio::EnsEMBL::Test::MultiTestDB;
+
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
+
+my $db = $multi->get_DBAdaptor( "core" );
+#debug( "Test database instatiated" );
+ok( $db , 'Test database instantiated');
+
+my $sa = $db->get_SliceAdaptor;
+my $ga = $db->get_GeneAdaptor;
+my $slice = $sa->fetch_by_region('chromosome', '1', 0, 10000000 );
+my @genes = @{$ga->fetch_all_by_Slice($slice)};
+my $num_genes = scalar(@genes);
+ok($num_genes, 'Failed to find genes on test Slice, please Slice redefine in test');
+
+
+SKIP:{
+ #test fetch_Iterator_by_Slice and implicitly fetch_Iterator_by_Slice_method
+ my $gi;
+
+ if(! $num_genes){
+ skip 'Skipping fetch_Iterator_by_Slice test due to lack of genes on slice, '.
+ 'please redefined slice in test', 1;
+ }
+ else{
+ #define chunk size such that the first chunk has no genes
+ #and the first gene crosses the 2nd and 3rd chunk;
+ my $chunk_size = ($genes[0]->seq_region_start + 10)/2;
+ $gi = $ga->fetch_Iterator_by_Slice($slice, undef, $chunk_size);
+ }
+
+ my $got_gi = isa_ok($gi, 'Bio::EnsEMBL::Utils::Iterator', 'Gene Iterator');
+
+ SKIP:{
+ my $gene_cnt = 0;
+
+ if(! $got_gi){
+ skip 'Skipping fetch_Iterator_by_Slice test as failed to fetch Gene Iterator', 1;
+ }
+ else{
+ my $gene;
+
+ while($gene = $gi->next){
+ $gene_cnt++;
+ }
+ }
+
+ ok(($gene_cnt == $num_genes), 'fetch_Iterator_by_Slice returned correct number of features');
+ }
+}
+
+done_testing();
--
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