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ensembl-gh-mirror
ensembl
Commits
766a9ad7
Commit
766a9ad7
authored
8 years ago
by
Matthew Laird
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We need to asign the slice when creating a fake exon in the tests
parent
182eb849
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2 merge requests
!130
Test/transcript mapper
,
!130
Test/transcript mapper
Changes
1
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1 changed file
modules/t/exon.t
+7
-6
7 additions, 6 deletions
modules/t/exon.t
with
7 additions
and
6 deletions
modules/t/exon.t
+
7
−
6
View file @
766a9ad7
...
...
@@ -360,24 +360,25 @@ SKIP: {
my
$base_transcript
=
Bio::EnsEMBL::
Transcript
->
new
(
-
START
=>
99
,
-
END
=>
1759
,
-
STRAND
=>
1
,
-
SLICE
=>
$base_slice
);
my
$start_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
99
,
-
END
=>
319
,
-
STRAND
=>
1
,
-
STABLE_ID
=>
'
Exon1
');
my
$start_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
99
,
-
END
=>
319
,
-
STRAND
=>
1
,
-
STABLE_ID
=>
'
Exon1
'
,
-
SLICE
=>
$base_slice
);
throws_ok
{
$start_exon
->
rank
(
$base_transcript
)
}
qr/does not have/
,
"
No exons in transcript
";
$base_transcript
->
add_Exon
(
$start_exon
);
is
(
$start_exon
->
rank
(
$base_transcript
),
1
,
"
Start exon in position 1
");
my
$end_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
1267
,
-
END
=>
1759
,
-
STRAND
=>
1
,
-
STABLE_ID
=>
'
Exon2
');
my
$end_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
1267
,
-
END
=>
1759
,
-
STRAND
=>
1
,
-
STABLE_ID
=>
'
Exon2
'
,
-
SLICE
=>
$base_slice
);
throws_ok
{
$end_exon
->
rank
(
$base_transcript
)
}
qr/does not belong/
,
"
Exon does not belong to transcript
";
$base_transcript
->
add_Exon
(
$end_exon
);
$base_transcript
->
translation
(
Bio::EnsEMBL::
Translation
->
new
(
-
START_EXON
=>
$start_exon
,
-
SEQ_START
=>
155
,
-
END_EXON
=>
$end_exon
,
-
SEQ_END
=>
87
));
is
(
$start_exon
->
cdna_coding_start
(
$base_transcript
),
155
,
'
Coding starts at 155bp into the first exon
');
is
(
$start_exon
->
cdna_coding_end
(
$base_transcript
),
221
,
'
Coding ends at 221bp in the first exon (at the exon end)
');
is
(
$start_exon
->
coding_region_start
(
$base_transcript
),
(
99
+
155
)
-
1
,
'
Coding starts at an offset of 99bp plus coding start
');
...
...
@@ -406,9 +407,9 @@ SKIP: {
);
my
$start_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
4205
,
-
END
=>
5661
,
-
STRAND
=>
-
1
);
my
$start_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
4205
,
-
END
=>
5661
,
-
STRAND
=>
-
1
,
-
SLICE
=>
$base_slice
);
$base_transcript
->
add_Exon
(
$start_exon
);
my
$end_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
672
,
-
END
=>
3363
,
-
STRAND
=>
-
1
);
my
$end_exon
=
Bio::EnsEMBL::
Exon
->
new
(
-
START
=>
672
,
-
END
=>
3363
,
-
STRAND
=>
-
1
,
-
SLICE
=>
$base_slice
);
$base_transcript
->
add_Exon
(
$end_exon
);
$base_transcript
->
translation
(
Bio::EnsEMBL::
Translation
->
new
(
...
...
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