Commit 721103ef authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

Updated to match new alt-allele error messages.

parent 24331721
......@@ -3,7 +3,7 @@ use warnings;
use Test::More;
use Test::Exception;
use Data::Dumper;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
......@@ -512,7 +512,7 @@ $gene = $ga->fetch_by_dbID(18256);
my $alt_genes = $gene->get_all_alt_alleles();
ok($gene->is_reference == 1);
#diag Dumper($alt_genes);
ok(scalar(@$alt_genes) == 3);
# expect the following alleles
......@@ -522,7 +522,7 @@ for my $gene (@$alt_genes) {
$ok = $ok && $gene_ids{$gene->dbID()};
$ok = $ok && !($gene->is_reference);
}
ok($ok);
ok($ok, "Retrieved alt alleles have correct dbIDs");
#
# test storing a new allele group
......@@ -544,13 +544,13 @@ push(@alt_genes, $ga->fetch_by_dbID(18270));
push(@alt_genes, $ga->fetch_by_dbID(18271));
push(@alt_genes, $ga->fetch_by_dbID(18272));
capture_std_streams(
warns_like(
sub {
my ($stdout_ref, $stderr_ref) = @_;
# my ($stdout_ref, $stderr_ref) = @_;
$ga->store_alt_alleles(\@alt_genes);
my $check = qr/.+ alternative .+ reference sequence .+ Ignoring/;
like(${$stderr_ref}, $check, 'Checking we are still warning about multiple alt_alleles on refs');
});
# my $check = qr/.+alternative.+reference\ssequence.+Ignoring/;
# like(${$stderr_ref}, $check, 'Checking we are still warning about multiple alt_alleles on refs');
}, qr/.+alternative.+reference\ssequence.+Ignoring/, 'Checking we are still warning about multiple alt_alleles on refs');
$gene = $ga->fetch_by_dbID(18270);
$alt_genes = $gene->get_all_alt_alleles();
%gene_ids = (18271 => 1, 18272 => 1);
......
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