diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index 0d7c69c15395ad95619d4eceb18823bd37702111..f485d78677f185ef4132811e745d3d6555707517 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
@@ -745,6 +745,15 @@ FEATURE: while ( $sth->fetch() ) {
} ## end else [ if ( $dest_slice_strand...)]
+ # Throw away features off the end of the requested slice or on
+ # different seq_region.
+ if ( $seq_region_end < 1
+ || $seq_region_start > $dest_slice_length
+ || ($dest_slice_sr_id ne $seq_region_id))
+ {
+ next FEATURE;
+ }
+
$slice = $dest_slice;
} ## end if ( defined($dest_slice...))
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 2371efca2f5b23c277604148eb682d3ad3e8bfcd..f73403a8b799838687c8846a0d764ac66d0772ff 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -1706,6 +1706,15 @@ FEATURE: while ($sth->fetch()) {
} ## end else [ if ($dest_slice_strand...)]
+ # Throw away features off the end of the requested slice or on
+ # different seq_region.
+ if ( $seq_region_end < 1
+ || $seq_region_start > $dest_slice_length
+ || ($dest_slice_sr_id ne $seq_region_id))
+ {
+ next FEATURE;
+ }
+
$slice = $dest_slice;
} ## end if (defined($dest_slice...))
diff --git a/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
index b89ed5adc8f5e92766594f9cd2de30a0fec55864..0da22bef2e3400ab8d6e0f09e05b05f17eeb4572 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
@@ -303,24 +303,112 @@ sub _objs_from_sth {
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
- if($dest_slice_start != 1 || $dest_slice_strand != 1) {
- if($dest_slice_strand == 1) {
- $seq_region_start = $seq_region_start - $dest_slice_start + 1;
- $seq_region_end = $seq_region_end - $dest_slice_start + 1;
- } else {
- my $tmp_seq_region_start = $seq_region_start;
- $seq_region_start = $dest_slice_end - $seq_region_end + 1;
- $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
- $seq_region_strand *= -1;
- }
- }
-
- #throw away features off the end of the requested slice
- if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
- ( $dest_slice_seq_region_id != $seq_region_id )) {
-# print STDERR "IGNORED DUE TO CUTOFF $dest_slice_seq_region_id ne $seq_region_id . $sr_name\n";
+ my $seq_region_len = $dest_slice->seq_region_length();
+
+ if ($dest_slice_strand == 1) { # Positive strand
+
+ $seq_region_start = $seq_region_start - $dest_slice_start + 1;
+ $seq_region_end = $seq_region_end - $dest_slice_start + 1;
+
+ if ($dest_slice->is_circular()) {
+ # Handle cicular chromosomes.
+
+ if ($seq_region_start > $seq_region_end) {
+ # Looking at a feature overlapping the chromsome origin.
+
+ if ($seq_region_end > $dest_slice_start) {
+
+ # Looking at the region in the beginning of the
+ # chromosome.
+ $seq_region_start -= $seq_region_len;
+ }
+
+ if ($seq_region_end < 0) {
+ $seq_region_end += $seq_region_len;
+ }
+
+ } else {
+
+ if ( $dest_slice_start > $dest_slice_end
+ && $seq_region_end < 0) {
+ # Looking at the region overlapping the chromosome
+ # origin and a feature which is at the beginning of the
+ # chromosome.
+ $seq_region_start += $seq_region_len;
+ $seq_region_end += $seq_region_len;
+ }
+ }
+
+ } ## end if ($dest_slice->is_circular...)
+
+ } else { # Negative strand
+
+ my $start = $dest_slice_end - $seq_region_end + 1;
+ my $end = $dest_slice_end - $seq_region_start + 1;
+
+ if ($dest_slice->is_circular()) {
+
+ if ($dest_slice_start > $dest_slice_end) {
+ # slice spans origin or replication
+
+ if ($seq_region_start >= $dest_slice_start) {
+ $end += $seq_region_len;
+ $start += $seq_region_len
+ if $seq_region_end > $dest_slice_start;
+
+ } elsif ($seq_region_start <= $dest_slice_end) {
+ # do nothing
+ } elsif ($seq_region_end >= $dest_slice_start) {
+ $start += $seq_region_len;
+ $end += $seq_region_len;
+
+ } elsif ($seq_region_end <= $dest_slice_end) {
+
+ $end += $seq_region_len
+ if $end < 0;
+
+ } elsif ($seq_region_start > $seq_region_end) {
+
+ $end += $seq_region_len;
+
+ } else {
+
+ }
+
+ } else {
+
+ if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
+ # do nothing
+ } elsif ($seq_region_start > $seq_region_end) {
+ if ($seq_region_start <= $dest_slice_end) {
+
+ $start -= $seq_region_len;
+
+ } elsif ($seq_region_end >= $dest_slice_start) {
+ $end += $seq_region_len;
+
+ } else {
+
+ }
+ }
+ }
+
+ }
+
+ $seq_region_start = $start;
+ $seq_region_end = $end;
+ $seq_region_strand *= -1;
+
+ } ## end else [ if ($dest_slice_strand...)]
+
+ # Throw away features off the end of the requested slice or on
+ # different seq_region.
+ if ( $seq_region_end < 1
+ || $seq_region_start > $dest_slice_length
+ || ($dest_slice_seq_region_id ne $seq_region_id)) {
next FEATURE;
}
+
$slice = $dest_slice;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 000e9f2b615a04a47f36e1223b7dafc54b9385d1..8aaea4181d1011f646eb95a301460d69d413c794 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -1693,6 +1693,15 @@ sub _objs_from_sth {
} ## end else [ if ( $dest_slice_strand...)]
+ # Throw away features off the end of the requested slice or on
+ # different seq_region.
+ if ( $seq_region_end < 1
+ || $seq_region_start > $dest_slice_length
+ || ($dest_slice_sr_id ne $seq_region_id))
+ {
+ next FEATURE;
+ }
+
$slice = $dest_slice;
}