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ensembl-gh-mirror
ensembl
Commits
fa6cb567
Commit
fa6cb567
authored
Nov 12, 2015
by
Magali Ruffier
Browse files
use explicit slice with adaptor
parent
eddd8762
Changes
1
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4 additions
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9 deletions
+4
-9
modules/t/bedSerialiser.t
modules/t/bedSerialiser.t
+4
-9
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modules/t/bedSerialiser.t
View file @
fa6cb567
...
...
@@ -52,20 +52,15 @@ my $ta = $dba->get_TranscriptAdaptor();
}
{
my
$cs
=
$dba
->
get_CoordSystemAdaptor
()
->
fetch_by_name
('
chromosome
');
my
$sa
=
$dba
->
get_SliceAdaptor
();
my
$slice
=
$sa
->
fetch_by_region
('
chromosome
',
12
,
1
,
10
);
my
$feature
=
Bio::EnsEMBL::
Feature
->
new
(
-
SLICE
=>
Bio::EnsEMBL::
Slice
->
new
(
-
COORD_SYSTEM
=>
$cs
,
-
SEQ
=>
('
A
'
x10
),
-
SEQ_REGION_NAME
=>
'
wibble
',
-
START
=>
1
,
-
END
=>
10
),
-
SLICE
=>
$slice
,
-
START
=>
1
,
-
END
=>
10
,
-
STRAND
=>
1
,
);
my
$expected
=
qq{
wibble
\t0\t10\t\t1000\t+\n}
;
my
$expected
=
qq{
12
\t0\t10\t\t1000\t+\n}
;
assert_bed
(
$feature
,
$expected
,
'
Default feature should seralise without attributes
');
}
...
...
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