diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index b9886d612a31dd061504db28c5777a49867d5097..5be12d22c1eb2d84e8e5b2e8f4dfa1d21a00ac07 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -170,12 +170,13 @@ sub fetch_by_region {
throw('start [$start] must be less than or equal to end [$end]');
}
- return Bio::EnsEMBL::Slice->new(-COORD_SYSTEM => $coord_system,
- -SEQ_REGION_NAME => $seq_region_name,
- -START => $start,
- -END => $end,
- -STRAND => $strand,
- -ADAPTOR => $self);
+ return Bio::EnsEMBL::Slice->new(-COORD_SYSTEM => $coord_system,
+ -SEQ_REGION_NAME => $seq_region_name,
+ -SEQ_REGION_LENGTH => $length,
+ -START => $start,
+ -END => $end,
+ -STRAND => $strand,
+ -ADAPTOR => $self);
}
@@ -269,12 +270,13 @@ sub fetch_by_seq_region_id {
$self->{'_name_cache'}->{$key} = [$seq_region_id, $length];
}
- return Bio::EnsEMBL::Slice->new(-COORD_SYSTEM => $cs,
- -SEQ_REGION_NAME => $name,
- -START => 1,
- -END => $length,
- -STRAND => 1,
- -ADAPTOR => $self);
+ return Bio::EnsEMBL::Slice->new(-COORD_SYSTEM => $cs,
+ -SEQ_REGION_NAME => $name,
+ -SEQ_REGION_LENGTH => $length,
+ -START => 1,
+ -END => $length,
+ -STRAND => 1,
+ -ADAPTOR => $self);
}
@@ -535,12 +537,13 @@ sub fetch_all {
#any remainder gets added to the last slice of the seq_region
$end = $length if($i == $number-1);
- push @out, Bio::EnsEMBL::Slice->new(-START => $start,
- -END => $end,
- -STRAND => 1,
- -SEQ_REGION_NAME => $name,
- -COORD_SYSTEM => $cs,
- -ADAPTOR => $self);
+ push @out, Bio::EnsEMBL::Slice->new(-START => $start,
+ -END => $end,
+ -STRAND => 1,
+ -SEQ_REGION_NAME => $name,
+ -SEQ_REGION_LENGTH => $length,
+ -COORD_SYSTEM => $cs,
+ -ADAPTOR => $self);
$start += $multiple;
}
}
@@ -588,6 +591,7 @@ sub fetch_all_non_redundant {
-END => $length,
-STRAND => 1,
-SEQ_REGION_NAME => $name,
+ -SEQ_REGION_LENGTH => $length,
-COORD_SYSTEM => $cs,
-ADAPTOR => $self);
}
@@ -754,6 +758,8 @@ sub fetch_by_gene_stable_id {
The feature to fetch the slice around
Arg [2] : int size (optional)
The desired number of flanking basepairs around the feature.
+ The size may also be provided as a percentage of the feature
+ size such as 200% or 80.5%.
Example : $slice = $slice_adaptor->fetch_by_Feature($feat, 100);
Description: Retrieves a slice around a specific feature. All this really
does is return a resized version of the slice that the feature
@@ -803,19 +809,22 @@ sub fetch_by_Feature{
}
}
-## Size may be stored as a %age of the length of the feature
-## Size = 100% gives no context
-## Size = 200% gives context - 50% the size of the feature either side of feature
+ ## Size may be stored as a %age of the length of the feature
+ ## Size = 100% gives no context
+ ## Size = 200% gives context - 50% the size of the feature either side of
+ ## feature
$size = int( ($1-100)/200 * ($fend-$fstart+1) ) if( $size =~/([\d+\.]+)%/ );
#return a new slice covering the region of the feature
- return Bio::EnsEMBL::Slice->new(-seq_region_name => $slice->seq_region_name,
- -coord_system => $slice->coord_system,
- -start => $fstart - $size,
- -end => $fend + $size,
- -strand => 1,
- -adaptor => $self);
+ return Bio::EnsEMBL::Slice->new
+ (-seq_region_name => $slice->seq_region_name,
+ -seq_region_length => $slice->seq_region_length,
+ -coord_system => $slice->coord_system,
+ -start => $fstart - $size,
+ -end => $fend + $size,
+ -strand => 1,
+ -adaptor => $self);
}
@@ -989,24 +998,26 @@ sub fetch_normalized_slice_projection {
for my $coord ( @linked ) {
if( $coord->isa( "Bio::EnsEMBL::Mapper::Gap" )) {
my $exc_slice = Bio::EnsEMBL::Slice->new
- (-START => $coord->start(),
- -END => $coord->end(),
- -STRAND => $slice->strand(),
- -COORD_SYSTEM => $slice->coord_system(),
- -ADAPTOR => $self,
- -SEQ_REGION_NAME => $slice->seq_region_name);
+ (-START => $coord->start(),
+ -END => $coord->end(),
+ -STRAND => $slice->strand(),
+ -COORD_SYSTEM => $slice->coord_system(),
+ -ADAPTOR => $self,
+ -SEQ_REGION_NAME => $slice->seq_region_name(),
+ -SEQ_REGION_LENGTH => $slice->seq_region_length());
push( @out, [ $rel_start, $coord->length()+$rel_start-1,
$exc_slice ] );
} else {
my $exc_slice = $self->fetch_by_seq_region_id( $coord->id() );
my $exc2_slice = Bio::EnsEMBL::Slice->new
(
- -START => $coord->start(),
- -END => $coord->end(),
- -STRAND => $coord->strand(),
- -SEQ_REGION_NAME => $exc_slice->seq_region_name(),
- -COORD_SYSTEM => $exc_slice->coord_system(),
- -ADAPTOR => $self
+ -START => $coord->start(),
+ -END => $coord->end(),
+ -STRAND => $coord->strand(),
+ -SEQ_REGION_NAME => $exc_slice->seq_region_name(),
+ -SEQ_REGION_LENGTH => $exc_slice->seq_region_length(),
+ -COORD_SYSTEM => $exc_slice->coord_system(),
+ -ADAPTOR => $self
);
push( @out, [ $rel_start, $coord->length() + $rel_start - 1,
@@ -1033,7 +1044,8 @@ sub fetch_normalized_slice_projection {
start at 1, and must have a valid seq_region name and coordinate
system. The attached coordinate system must already be stored in
the database. The sequence region is assumed to start at 1 and
- to have a length equalling the length of the slice.
+ to have a length equalling the length of the slice. The end of
+ the slice must equal the seq_region_length.
If the slice coordinate system is the sequence level coordinate
system then the seqref argument must also be passed. If the
slice coordinate system is NOT a sequence level coordinate
@@ -1050,6 +1062,7 @@ sub fetch_normalized_slice_projection {
match the slice length.
throw if the SQL insert fails (e.g. on duplicate seq region)
throw if slice argument is not passed
+ throw if the slice end is not equal to seq_region_length
Caller : database loading scripts
=cut
@@ -1081,6 +1094,10 @@ sub store {
throw("Slice must have start==1 and strand==1.");
}
+ if($slice->end() != $slice->seq_region_length()) {
+ throw("Slice must have end==seq_region_length");
+ }
+
my $sr_len = $slice->length();
my $sr_name = $slice->seq_region_name();