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ensembl-gh-mirror
ensembl-rest
Commits
f5a480ac
Commit
f5a480ac
authored
9 years ago
by
William McLaren
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use get_best_compara_DBAdaptor as recommended by compara
parent
a980c259
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1 merge request
!87
Fixes so Conservation plugin works (master)
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1 changed file
lib/EnsEMBL/REST/Controller/VEP.pm
+3
-2
3 additions, 2 deletions
lib/EnsEMBL/REST/Controller/VEP.pm
with
3 additions
and
2 deletions
lib/EnsEMBL/REST/Controller/VEP.pm
+
3
−
2
View file @
f5a480ac
...
...
@@ -93,8 +93,9 @@ sub get_species : Chained('/') PathPart('vep') CaptureArgs(1) {
}
# get compara adaptors
$c
->
stash
(
mlssa
=>
$c
->
model
('
Registry
')
->
get_adaptor
(
'
Multi
',
'
compara
',
'
MethodLinkSpeciesSet
'
)
);
$c
->
stash
(
cosa
=>
$c
->
model
('
Registry
')
->
get_adaptor
(
'
Multi
',
'
compara
',
'
ConservationScore
'
)
);
my
$compara_dba
=
$c
->
model
('
Registry
')
->
get_best_compara_DBAdaptor
(
$species
,
$c
->
request
()
->
param
('
compara
'));
$c
->
stash
(
mlssa
=>
$compara_dba
->
get_MethodLinkSpeciesSetAdaptor
()
);
$c
->
stash
(
cosa
=>
$compara_dba
->
get_ConservationScoreAdaptor
()
);
}
catch
{
$c
->
log
->
fatal
(
qq{problem making Bio::EnsEMBL::Variation::VariationFeature object}
);
$c
->
go
('
ReturnError
',
'
from_ensembl
',
[
qq{$_}
])
if
$_
=~
/STACK/
;
...
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