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ensembl-gh-mirror
ensembl-io
Commits
58be8878
Commit
58be8878
authored
Sep 28, 2018
by
Tiago Grego
Browse files
tab removal, biotype bug
parent
58cf80a6
Changes
1
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1 changed file
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37 additions
and
30 deletions
+37
-30
modules/Bio/EnsEMBL/IO/Translator/BulkFetcherFeature.pm
modules/Bio/EnsEMBL/IO/Translator/BulkFetcherFeature.pm
+37
-30
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modules/Bio/EnsEMBL/IO/Translator/BulkFetcherFeature.pm
View file @
58be8878
...
...
@@ -40,36 +40,37 @@ use Carp;
use
Bio::EnsEMBL::Utils::
RDF
qw/feature_uri/
;
use
Bio::EnsEMBL::Utils::RDF::
Mapper
;
my
%field_callbacks
=
(
version
=>
'
version
',
production_name
=>
'
production_name
',
id_org_short
=>
'
id_org_short
',
lod_uri
=>
'
lod_uri
',
type
=>
'
type
',
id
=>
'
id
',
name
=>
'
name
',
description
=>
'
description
',
seq_region_name
=>
'
seq_region_name
',
cs_name
=>
'
coord_system_name
',
cs_version
=>
'
coord_system_version
',
start
=>
'
start
',
end
=>
'
end
',
strand
=>
'
strand
',
biotype
=>
'
biotype
',
rank
=>
'
rank
',
taxon_id
=>
'
taxon_id
',
uri
=>
'
uri
',
synonyms
=>
'
synonyms
',
provenance
=>
'
provenance
',
homologues
=>
'
homologues
',
xrefs
=>
'
xrefs
',
dbname
=>
'
dbname
',
homologues
=>
'
homologues
',
transcripts
=>
'
transcripts
',
exons
=>
'
exons
',
translations
=>
'
translations
',
protein_features
=>
'
protein_features
',
so_term
=>
'
so_term
'
);
my
%field_callbacks
=
(
version
=>
'
version
',
production_name
=>
'
production_name
',
id_org_short
=>
'
id_org_short
',
lod_uri
=>
'
lod_uri
',
type
=>
'
type
',
id
=>
'
id
',
name
=>
'
name
',
description
=>
'
description
',
seq_region_name
=>
'
seq_region_name
',
cs_name
=>
'
coord_system_name
',
cs_version
=>
'
coord_system_version
',
start
=>
'
start
',
end
=>
'
end
',
strand
=>
'
strand
',
biotype
=>
'
biotype
',
rank
=>
'
rank
',
taxon_id
=>
'
taxon_id
',
uri
=>
'
uri
',
synonyms
=>
'
synonyms
',
provenance
=>
'
provenance
',
homologues
=>
'
homologues
',
xrefs
=>
'
xrefs
',
dbname
=>
'
dbname
',
homologues
=>
'
homologues
',
transcripts
=>
'
transcripts
',
exons
=>
'
exons
',
translations
=>
'
translations
',
protein_features
=>
'
protein_features
',
so_term
=>
'
so_term
'
);
=head2 new
...
...
@@ -498,6 +499,12 @@ sub so_term {
my
$so_term
;
my
(
$type
,
$biotype
)
=
(
$self
->
type
(
$object
),
$self
->
biotype
(
$object
));
if
(
!
defined
$biotype
)
{
# warn "Could not find biotype for SO term mapping\n";
return
;
}
eval
{
if
(
$type
eq
'
gene
')
{
$so_term
=
$self
->
biotype_mapper
->
gene_biotype_to_name
(
$biotype
);
...
...
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