From 4b6598cd4e2316af16216a136577fd8d6f64c672 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 22 May 2012 16:29:51 +0000
Subject: [PATCH] ENSCORESW-159 test case. Adding a -ve strand example based on
the 66 human release
---
modules/t/exon.t | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/modules/t/exon.t b/modules/t/exon.t
index 276b3ede6c..ffa4ba1fe7 100644
--- a/modules/t/exon.t
+++ b/modules/t/exon.t
@@ -330,4 +330,44 @@ ok( $species eq 'homo_sapiens' && $object_type eq 'Exon');
is($end_exon->coding_region_end($base_transcript), (1267+87)-1, 'Seq region location end is offsetted by exon coding length');
}
+# Checking the reverse strand. Taken from ENST00000321407 in E! 66 with 66
+# API to check for regressions
+{
+ my $base_cs = Bio::EnsEMBL::CoordSystem->new(-NAME => 'chromosome', -RANK => 1);
+ my $base_slice = Bio::EnsEMBL::Slice->new(
+ -COORD_SYSTEM => $base_cs, -SEQ_REGION_NAME => 'a',
+ -STRAND => 1, -START => 1, -END => 6000, -SEQ => 'A'x6000,
+ -SEQ_REGION_LENGTH => 6000
+ );
+ my $base_transcript = Bio::EnsEMBL::Transcript->new(
+ -START => 672,
+ -END => 5661,
+ -SLICE => $base_slice,
+ -STRAND => -1
+ );
+
+
+ my $start_exon = Bio::EnsEMBL::Exon->new(-START => 4205, -END => 5661, -STRAND => -1);
+ $base_transcript->add_Exon($start_exon);
+ my $end_exon = Bio::EnsEMBL::Exon->new(-START => 672, -END => 3363, -STRAND => -1);
+ $base_transcript->add_Exon($end_exon);
+
+ $base_transcript->translation(Bio::EnsEMBL::Translation->new(
+ -START_EXON => $start_exon,
+ -SEQ_START => 426,
+ -END_EXON => $end_exon,
+ -SEQ_END => 1296
+ ));
+
+ is($start_exon->cdna_coding_start($base_transcript), 426, 'CDNA start equals SEQ_START');
+ is($start_exon->cdna_coding_end($base_transcript), 1457, 'CDNA end equals SEQ_START plus exon length');
+ is($start_exon->coding_region_start($base_transcript), 4205, 'Coding region start is start of first exon');
+ is($start_exon->coding_region_end($base_transcript), 5236, 'Coding region end is start of first exon plus its length');
+
+ is($end_exon->cdna_coding_start($base_transcript), 1458, 'CDNA coding start equals END of first Exon + 1');
+ is($end_exon->cdna_coding_end($base_transcript), 2753, 'CDNA coding end equals start plus its length into the last exon');
+ is($end_exon->coding_region_start($base_transcript), 2068, 'Start is the end of the last exon minus the coding length');
+ is($end_exon->coding_region_end($base_transcript), 3363, 'End is the same as the end exon end');
+}
+
done_testing();
\ No newline at end of file
--
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