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ensembl-gh-mirror
ensembl
Commits
d316790a
Commit
d316790a
authored
11 years ago
by
Magali Ruffier
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removed test on patch slice as data is not compatible with other tests
parent
77092de8
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1 changed file
modules/t/assemblyExceptionFeature.t
+0
-25
0 additions, 25 deletions
modules/t/assemblyExceptionFeature.t
with
0 additions
and
25 deletions
modules/t/assemblyExceptionFeature.t
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0
−
25
View file @
d316790a
...
...
@@ -43,19 +43,10 @@ is(ref($aef->adaptor), 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', "
# fetch all
my
$chr_slice
=
$dba
->
get_SliceAdaptor
->
fetch_by_region
('
chromosome
',
'
20_HAP1
');
my
$ref_slice
=
$dba
->
get_SliceAdaptor
->
fetch_by_region
('
chromosome
',
'
X
');
my
$patch_slice
=
$dba
->
get_SliceAdaptor
->
fetch_by_region
('
supercontig
',
'
HG480_HG481_PATCH
');
my
@features
=
@
{
$aefa
->
fetch_all_by_Slice
(
$chr_slice
)};
is
(
@features
,
1
,
"
Fetched one assembly exception feature for 20_HAP1
");
my
@ref_features
=
@
{
$aefa
->
fetch_all_by_Slice
(
$ref_slice
)};
is
(
@ref_features
,
1
,
"
Fetched one assembly exception features for chromosome X
");
my
@patch_features
=
@
{
$aefa
->
fetch_all_by_Slice
(
$patch_slice
)
};
is
(
@patch_features
,
1
,
"
Fetched one assembly exception for HG480_HG481_PATCH
");
foreach
my
$f
(
@features
)
{
debug
(
"
Feature:
"
.
$f
->
slice
->
seq_region_name
.
"
"
.
$f
->
start
.
"
"
.
$f
->
end
.
"
"
.
$f
->
type
);
...
...
@@ -64,22 +55,6 @@ foreach my $f (@features) {
$as
->
start
.
"
"
.
$as
->
end
);
}
foreach
my
$f
(
@ref_features
)
{
debug
(
"
Feature:
"
.
$f
->
slice
->
seq_region_name
.
"
"
.
$f
->
start
.
"
"
.
$f
->
end
.
"
"
.
$f
->
type
);
my
$as
=
$f
->
alternate_slice
();
debug
("
Alternate slice:
"
.
$as
->
seq_region_name
.
"
"
.
$as
->
start
.
"
"
.
$as
->
end
);
}
foreach
my
$f
(
@patch_features
)
{
debug
(
"
Feature:
"
.
$f
->
slice
->
seq_region_name
.
"
"
.
$f
->
start
.
"
"
.
$f
->
end
.
"
"
.
$f
->
type
);
my
$as
=
$f
->
alternate_slice
();
debug
("
Alternate slice:
"
.
$as
->
seq_region_name
.
"
"
.
$as
->
start
.
"
"
.
$as
->
end
);
}
my
(
$f
)
=
@features
;
is
(
$f
->
display_id
,
$f
->
alternate_slice
->
seq_region_name
,
"
Feature display id matches feature's alternate slice name
");
...
...
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