From c102da6d66a8bee09f2da0e4a0cbcf9ad5a1e5a4 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 14 Aug 2012 09:09:56 +0000
Subject: [PATCH] Test cases now pass, we have a capture warns asserting for
known bad scenarios and use the Test::Builder code to see if we want to do to
screen warning for test cases. Not sure how un # lines in TAP are dealt with;
we may want to substitute STDOUT/STDERR for something which can delegate to
Test::Builder for note()
---
.../Bio/EnsEMBL/Utils/TranscriptSelector.pm | 4 +--
modules/t/transcriptSelector.t | 36 +++++++++++--------
2 files changed, 23 insertions(+), 17 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm b/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm
index d02a6e458b..4e4a8569d4 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm
@@ -267,8 +267,8 @@ sub check_Ens_trans_against_CCDS {
. " found match "
. $ext_gene->display_id
. " in CCDS DB.\n" if $self->{'verbose'};
- if ($ext_gene->display_id !~ /^CCDS/) {
- throw ("Database does not appear to contain CCDS IDs. Possible configuration problem with CCDS source.");
+ if ($ext_gene->stable_id !~ /^CCDS/) {
+ throw (sprintf("Database does not appear to contain CCDS IDs. Possible configuration problem with CCDS source. Found ID %s", $ext_gene->stable_id()));
}
return 1;
}
diff --git a/modules/t/transcriptSelector.t b/modules/t/transcriptSelector.t
index 96abce345d..4f0bf332d9 100644
--- a/modules/t/transcriptSelector.t
+++ b/modules/t/transcriptSelector.t
@@ -2,6 +2,7 @@ use strict;
use warnings;
use Test::More;
+use Test::Builder;
use Test::Exception;
use Test::MockObject;
use Test::MockObject::Extends;
@@ -13,27 +14,33 @@ use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::CoordSystem;
use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::Test::TestUtils;
-my $transcript_selector = Bio::EnsEMBL::Utils::TranscriptSelector->new(undef, 'VERBOSE');
+my $verbose = Test::Builder->new()->no_diag() ? 0 : 1;
+
+my $transcript_selector;
+
+warns_like
+ { $transcript_selector = Bio::EnsEMBL::Utils::TranscriptSelector->new(undef, $verbose) }
+ qr/Running without CCDS DB/, 'Checking we warn about the lack of a CCDS DB';
# Test the sorting algorithm
# encoded arrays as follows:
#[transcript dbID, source , biotype, translation length, transcript length, stable ID]
my $sortables = [
- [qw( a 1 1 500 250 ENST7 )],
- [qw( b 2 1 500 250 ENST6 )],
- [qw( c 3 1 500 250 ENST5 )],
- [qw( d 1 1 450 250 ENST4 )],
- [qw( e 1 1 500 250 ENST3 )],
- [qw( f 3 3 0 700 ENST2 )],
- [qw( g 3 3 0 700 ENST1 )],
+ [qw( a 1 1 1 500 250 ENST7 )],
+ [qw( b 1 2 1 500 250 ENST6 )],
+ [qw( c 1 3 1 500 250 ENST5 )],
+ [qw( d 1 1 1 450 250 ENST4 )],
+ [qw( e 1 1 1 500 250 ENST3 )],
+ [qw( f 0 3 3 0 700 ENST2 )],
+ [qw( g 0 3 3 0 700 ENST1 )],
];
my $sorted = $transcript_selector->sort_into_canonical_order($sortables);
-print "Sorted order:\n";
-print join(',',@$sorted);
-print "\n";
+note "Sorted order";
+note join(',',@$sorted);
my $correct_order = [qw(e a d b c g f)];
is_deeply($sorted,$correct_order,'Canonical sort order');
@@ -155,6 +162,7 @@ my $gene = Bio::EnsEMBL::Gene->new(
-BIOTYPE => 'protein_coding',
-TRANSCRIPTS => $transcripts,
-SLICE => $slice,
+ -STABLE_ID => 'CCDS01'
);
my $mock_slice = Test::MockObject->new();
@@ -184,9 +192,7 @@ $mock_dba->mock('get_SliceAdaptor', sub {
return $mock_sa;
});
-
-$transcript_selector = Bio::EnsEMBL::Utils::TranscriptSelector->new($mock_dba, 'VERBOSE');
-
+$transcript_selector = Bio::EnsEMBL::Utils::TranscriptSelector->new($mock_dba, $verbose);
ok($transcript_selector->check_Ens_trans_against_CCDS($transcript2),'CCDS transcript lookup with good data');
ok($transcript_selector->check_Ens_trans_against_CCDS($transcript3) != 1,'CCDS transcript lookup with non-coding');
@@ -235,7 +241,7 @@ $gene = Bio::EnsEMBL::Gene->new(
-BIOTYPE => 'protein_coding',
-SLICE => $slice,
);
-$canonical_transcript = $transcript_selector->select_canonical_transcript_for_Gene($gene);
+warns_like { $canonical_transcript = $transcript_selector->select_canonical_transcript_for_Gene($gene)} qr/No transcripts attached/, 'Checking we warn about lack of transcripts against a gene';
note ($canonical_transcript);
is($canonical_transcript, undef, "Gene with no transcripts, fault tolerance");
--
GitLab