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ensembl-gh-mirror
ensembl
Commits
5fb74911
Commit
5fb74911
authored
Nov 16, 2015
by
Magali Ruffier
Browse files
deprecated broken method
parent
ce0593ce
Changes
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DEPRECATED.md
DEPRECATED.md
+1
-0
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+2
-22
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DEPRECATED.md
View file @
5fb74911
...
...
@@ -145,6 +145,7 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP
### Removed in Ensembl Release 84 ###
-
Bio::EnsEMBL::DBSQL::
**CoordSystemAdaptor**
::
*_fetch_by_attrib()*
-
Bio::EnsEMBL::DBSQL::
**CoordSystemAdaptor**
::
*_fetch_all_by_attrib()*
-
Bio::EnsEMBL::DBSQL::
**SliceAdaptor**
::
*fetch_by_band()*
-
Bio::EnsEMBL::DBSQL::
**MetaContainer**
::
*get_short_name()*
-
Bio::EnsEMBL::DBSQL::
**MetaContainer**
::
*get_max_assembly_contig()*
-
Bio::EnsEMBL::
**Exon**
::
*_get_stable_entry_info()*
...
...
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
View file @
5fb74911
...
...
@@ -1487,34 +1487,14 @@ sub is_circular {
=head2 fetch_by_band
Title : fetch_by_band
Usage :
Function: Does not work please use fetch_by_chr_band
Example :
Returns : Bio::EnsEMBL::Slice
Args : the band name
Status : AT RISK
Description : DEPRECATED. Use fetch_by_chr_band instead
=cut
sub
fetch_by_band
{
my
(
$self
,
$band
)
=
@_
;
my
$sth
=
$self
->
dbc
->
prepare
("
select s.name,max(k.seq_region_id)-min(k.seq_region_id, min(k.seq_region_start), max(k.seq_region_id)
"
.
"
from karyotype as k
"
.
"
where k.band like ? and k.seq_region_id = s.seq_region_id
");
$sth
->
bind_param
(
1
,"
$band
%
",
SQL_VARCHAR
);
$sth
->
execute
();
my
(
$seq_region_name
,
$discrepancy
,
$seq_region_start
,
$seq_region_end
)
=
$sth
->
fetchrow_array
;
if
(
$seq_region_name
&&
$discrepancy
>
0
)
{
throw
("
Band maps to multiple seq_regions
");
}
else
{
return
$self
->
fetch_by_region
('
toplevel
',
$seq_region_name
,
$seq_region_start
,
$seq_region_end
);
}
throw
("
Band not recognised in database
");
deprecate
("
fetch_by_band is deprecated and will be removed in e84. Please use fetch_by_chr_band instead.
");
}
=head2 fetch_by_chr_band
...
...
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