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ensembl-gh-mirror
ensembl
Commits
ede045fa
Commit
ede045fa
authored
Mar 19, 2019
by
Marek Szuba
Browse files
Convert stray tabs to spaces
parent
95953fbe
Changes
4
Hide whitespace changes
Inline
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Showing
4 changed files
with
22 additions
and
22 deletions
+22
-22
modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
+7
-7
modules/Bio/EnsEMBL/MicroRNA.pm
modules/Bio/EnsEMBL/MicroRNA.pm
+2
-2
modules/Bio/EnsEMBL/RNAProduct.pm
modules/Bio/EnsEMBL/RNAProduct.pm
+9
-9
modules/t/rnaProduct.t
modules/t/rnaProduct.t
+4
-4
No files found.
modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
View file @
ede045fa
...
...
@@ -136,8 +136,8 @@ sub fetch_all_by_external_name {
my
$entry_adaptor
=
$self
->
db
->
get_DBEntryAdaptor
();
my
@ids
=
$entry_adaptor
->
list_rnaproduct_ids_by_extids
(
$external_name
,
$external_db_name
,
$override
);
$external_db_name
,
$override
);
my
$transcript_adaptor
=
$self
->
db
()
->
get_TranscriptAdaptor
();
...
...
@@ -468,12 +468,12 @@ sub _fetch_direct_query {
my
$sql
=
sprintf
("
SELECT rp.rnaproduct_id, pt.code, rp.transcript_id,
"
.
"
rp.seq_start, rp.start_exon_id, rp.seq_end, rp.end_exon_id,
"
.
"
rp.seq_start, rp.start_exon_id, rp.seq_end, rp.end_exon_id,
"
.
"
rp.stable_id, rp.version, %s, %s
"
.
"
FROM rnaproduct rp JOIN rnaproduct_type pt
"
.
"
FROM rnaproduct rp JOIN rnaproduct_type pt
"
.
"
ON rp.rnaproduct_type_id = pt.rnaproduct_type_id
"
.
"
WHERE %s = ?
",
$rp_created_date
,
$rp_modified_date
,
$where_args
->
[
0
]);
.
"
WHERE %s = ?
",
$rp_created_date
,
$rp_modified_date
,
$where_args
->
[
0
]);
my
$sth
=
$self
->
prepare
(
$sql
);
$sth
->
bind_param
(
1
,
$where_args
->
[
1
],
$where_args
->
[
2
]);
$sth
->
execute
();
...
...
@@ -501,7 +501,7 @@ sub _obj_from_sth {
my
$transcript_adaptor
=
$self
->
db
()
->
get_TranscriptAdaptor
();
while
(
my
$row_ref
=
shift
@
{
$sql_data
})
{
my
(
$rnaproduct_id
,
$type_code
,
$transcript_id
,
$seq_start
,
$start_exon_id
,
$seq_end
,
$end_exon_id
,
$stable_id
,
$version
,
$created_date
,
$seq_end
,
$end_exon_id
,
$stable_id
,
$version
,
$created_date
,
$modified_date
)
=
@
{
$row_ref
};
if
(
!
defined
(
$rnaproduct_id
))
{
...
...
modules/Bio/EnsEMBL/MicroRNA.pm
View file @
ede045fa
...
...
@@ -134,8 +134,8 @@ sub arm {
my
$n_arms
=
scalar
@
{
$arm_attrs
};
if
(
$n_arms
>
0
)
{
if
(
$n_arms
>
1
)
{
throw
("
MicroRNA
"
.
$self
->
display_id
()
.
"
has multiple arm attributes
");
throw
("
MicroRNA
"
.
$self
->
display_id
()
.
"
has multiple arm attributes
");
}
$self
->
{'
arm
'}
=
$arm_attrs
->
[
0
]
->
value
();
}
...
...
modules/Bio/EnsEMBL/RNAProduct.pm
View file @
ede045fa
...
...
@@ -110,7 +110,7 @@ sub new { ## no critic (Subroutines::RequireArgUnpacking)
my
(
$seq_start
,
$seq_end
,
$start_exon
,
$end_exon
,
$stable_id
,
$version
,
$dbID
,
$adaptor
,
$seq
,
$created_date
,
$modified_date
)
=
rearrange
(["
SEQ_START
",
"
SEQ_END
",
"
START_EXON
",
"
END_EXON
",
rearrange
(["
SEQ_START
",
"
SEQ_END
",
"
START_EXON
",
"
END_EXON
",
"
STABLE_ID
",
"
VERSION
",
"
DBID
",
"
ADAPTOR
",
"
SEQ
",
"
CREATED_DATE
",
"
MODIFIED_DATE
"],
@
_
);
...
...
@@ -356,10 +356,10 @@ sub genomic_end {
if
(
$transcript
->
strand
()
>=
0
)
{
$self
->
{'
genomic_end
'}
=
$transcript
->
start
()
+
(
$self
->
end
()
-
1
);
$transcript
->
start
()
+
(
$self
->
end
()
-
1
);
}
else
{
$self
->
{'
genomic_end
'}
=
$transcript
->
end
()
-
(
$self
->
start
()
-
1
);
$transcript
->
end
()
-
(
$self
->
start
()
-
1
);
}
}
...
...
@@ -388,10 +388,10 @@ sub genomic_start {
if
(
$transcript
->
strand
()
>=
0
)
{
$self
->
{'
genomic_start
'}
=
$transcript
->
start
()
+
(
$self
->
start
()
-
1
);
$transcript
->
start
()
+
(
$self
->
start
()
-
1
);
}
else
{
$self
->
{'
genomic_start
'}
=
$transcript
->
end
()
-
(
$self
->
end
()
-
1
);
$transcript
->
end
()
-
(
$self
->
end
()
-
1
);
}
}
...
...
@@ -733,10 +733,10 @@ sub stable_id_version {
my
$vindex
=
rindex
(
$stable_id
,
'
.
');
(
$self
->
{
stable_id
},
$self
->
{
version
})
=
(
$vindex
>
0
?
(
substr
(
$stable_id
,
0
,
$vindex
),
substr
(
$stable_id
,
$vindex
+
1
))
:
$stable_id
,
undef
);
(
substr
(
$stable_id
,
0
,
$vindex
),
substr
(
$stable_id
,
$vindex
+
1
))
:
$stable_id
,
undef
);
}
return
$self
->
{
stable_id
}
.
(
$self
->
{
version
}
?
"
.
$self
->{version}
"
:
'');
...
...
modules/t/rnaProduct.t
View file @
ede045fa
...
...
@@ -57,12 +57,12 @@ subtest 'RNAProductTypeMapper tests' => sub {
is
(
$rpt_mapper
->
type_code_to_class
('
miRNA
'),
'
Bio::EnsEMBL::MicroRNA
',
'
Can map existing type ID to class
');
dies_ok
(
sub
{
$rpt_mapper
->
type_code_to_class
('
semprini
');
},
'
Exception thrown on unknown type ID
');
'
Exception thrown on unknown type ID
');
is
(
$rpt_mapper
->
class_to_type_code
('
Bio::EnsEMBL::RNAProduct
'),
'
generic
',
'
Can map existing class to type ID
');
dies_ok
(
sub
{
$rpt_mapper
->
class_to_type_code
('
Bio::EnsEMBL::Storable
');
},
'
Exception thrown on unknown rnaproduct class name
');
'
Exception thrown on unknown rnaproduct class name
');
};
...
...
@@ -327,7 +327,7 @@ subtest 'Attribute functionality' => sub {
is
(
scalar
@
{
$rp_nonsense
},
0
,
'
Get empty attribute list for nonsense code
');
dies_ok
(
sub
{
$rp
->
add_Attributes
({})
},
'
add_Attributes() dies on invalid argument type
');
'
add_Attributes() dies on invalid argument type
');
my
$n_attrs_before
=
scalar
@
{
$rp_all_attrs
};
my
$extra_attr1
=
Bio::EnsEMBL::
Attribute
->
new
(
...
...
@@ -354,7 +354,7 @@ subtest 'xref functionality' => sub {
cmp_ok
(
scalar
@
{
$xrefs
},
'
>
',
0
,
'
Got a non-empty list of DBEntries
');
dies_ok
(
sub
{
$rp
->
add_DBEntry
({})
},
'
add_DBEntry() dies on invalid argument type
');
'
add_DBEntry() dies on invalid argument type
');
my
$n_xrefs_before
=
scalar
@
{
$xrefs
};
my
$dbe
=
Bio::EnsEMBL::
DBEntry
->
new
(
...
...
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