From 317f7fe814c97ac82025f783215265134a0d5c1c Mon Sep 17 00:00:00 2001
From: Nathan Johnson <njohnson@ebi.ac.uk>
Date: Mon, 6 Jun 2011 10:32:16 +0000
Subject: [PATCH] corrected 0 start on slice
---
modules/t/iterator.t | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/modules/t/iterator.t b/modules/t/iterator.t
index 7cab29ff1d..6a5e426bdd 100644
--- a/modules/t/iterator.t
+++ b/modules/t/iterator.t
@@ -142,10 +142,21 @@ 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 );
+
+
+#Need to find Slice which genes are on
+#Do this via direct mysql or hardcode?
+#sql is unlikely to change
+
+my $sql = 'SELECT sr.name, g.seq_region_start from gene g, seq_region sr where g.seq_region_id = sr.seq_region_id order by g.seq_region_start limit 1';
+my ($sr_name, $sr_start) = @{$db->dbc->db_handle->selectrow_arrayref($sql)};
+my $slice = $sa->fetch_by_region('chromosome', $sr_name, 1, ($sr_start + 1000000));
my @genes = @{$ga->fetch_all_by_Slice($slice)};
+
+#Are there any genes in this test DB?
+
my $num_genes = scalar(@genes);
-ok($num_genes, 'Failed to find genes on test Slice, please Slice redefine in test');
+ok($num_genes, "Found $num_genes Gene(s) on test Slice");
SKIP:{
@@ -175,11 +186,12 @@ SKIP:{
my $gene;
while($gene = $gi->next){
- $gene_cnt++;
+ print $gene->stable_id."\n";
+ $gene_cnt++;
}
}
- ok(($gene_cnt == $num_genes), 'fetch_Iterator_by_Slice returned correct number of features');
+ ok(($gene_cnt == $num_genes), "fetch_Iterator_by_Slice returned correct number of features($gene_cnt == $num_genes)");
}
}
--
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