diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
index 8261d4dad203c6ab6853001da245765e780537bb..636c3b17f48999137f33ddd85d210b2356be7917 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
@@ -324,14 +324,108 @@ sub _remap {
# create new copies of successfully mapped feaatures with shifted start,
# end and strand
my ($new_start, $new_end);
- if($slice_strand == -1) {
- $new_start = $slice_end - $end + 1;
- $new_end = $slice_end - $start + 1;
- } else {
- $new_start = $start - $slice_start + 1;
- $new_end = $end - $slice_start + 1;
- }
+ # if($slice_strand == -1) {
+ # $new_start = $slice_end - $end + 1;
+ # $new_end = $slice_end - $start + 1;
+ # } else {
+ # $new_start = $start - $slice_start + 1;
+ # $new_end = $end - $slice_start + 1;
+ # }
+ my $seq_region_len = $slice->seq_region_length();
+
+ if ($slice_strand == 1) { # Positive strand
+
+ $new_start = $start - $slice_start + 1;
+ $new_end = $end - $slice_start + 1;
+
+ if ($slice->is_circular()) {
+ # Handle circular chromosomes.
+
+ if ($new_start > $new_end) {
+ # Looking at a feature overlapping the chromsome origin.
+
+ if ($new_end > $slice_start) {
+
+ # Looking at the region in the beginning of the
+ # chromosome.
+ $new_start -= $seq_region_len;
+ }
+
+ if ($new_end < 0) {
+ $new_end += $seq_region_len;
+ }
+
+ } else {
+
+ if ( $slice_start > $slice_end
+ && $new_end < 0) {
+ # Looking at the region overlapping the chromosome
+ # origin and a feature which is at the beginning of the
+ # chromosome.
+ $new_start += $seq_region_len;
+ $new_end += $seq_region_len;
+ }
+ }
+
+ } ## end if ($dest_slice->is_circular...)
+
+ } else { # Negative strand
+
+ my $new_start = $slice_end - $end + 1;
+ my $new_end = $slice_end - $start + 1;
+
+ if ($slice->is_circular()) {
+
+ if ($slice_start > $slice_end) {
+ # slice spans origin or replication
+
+ if ($start >= $slice_start) {
+ $new_end += $seq_region_len;
+ $new_start += $seq_region_len
+ if $end > $slice_start;
+
+ } elsif ($start <= $slice_end) {
+ # do nothing
+ } elsif ($end >= $slice_start) {
+ $new_start += $seq_region_len;
+ $new_end += $seq_region_len;
+
+ } elsif ($end <= $slice_end) {
+
+ $new_end += $seq_region_len
+ if $new_end < 0;
+
+ } elsif ($start > $end) {
+
+ $new_end += $seq_region_len;
+
+ } else {
+
+ }
+
+ } else {
+
+ if ($start <= $slice_end and $end >= $slice_start) {
+ # do nothing
+ } elsif ($start > $end) {
+ if ($start <= $slice_end) {
+
+ $new_start -= $seq_region_len;
+
+ } elsif ($end >= $slice_start) {
+ $new_end += $seq_region_len;
+
+ } else {
+
+ }
+ }
+ }
+
+ }
+
+ } ## end else [ if ($dest_slice_strand...)]
+
push @out, Bio::EnsEMBL::AssemblyExceptionFeature->new(
'-dbID' => $f->dbID,
'-start' => $new_start,
diff --git a/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
index 9f5cbb116c19922a06864fac7c529c1cf9ccc209..1c2839612ec9b5f7a164bb07fb8443babb1d4323 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
@@ -501,25 +501,112 @@ FEATURE:
# If a destination slice was provided, convert the coords. If the
# dest_slice starts at 1 and is forward strand, nothing needs doing.
if ( defined($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;
- $seq_region_strand = -$seq_region_strand;
- }
+ 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;
- # 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 ne $seq_region_id ) )
+ } elsif ($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.
+ if ( $seq_region_end < 1
+ || $seq_region_start > $dest_slice_length
+ || ( $dest_slice_seq_region_id ne $seq_region_id ) )
{
next FEATURE;
}
- }
+
$slice = $dest_slice;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
index 216829a42d4115942f82a147a9ba733bf0b7f8ba..09c27241fbcf692c86572331304fa5dfb664b404 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
@@ -469,20 +469,106 @@ sub _objs_from_sth {
#
# If a destination slice was provided convert the coords
- # If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if ($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;
- }
- }
+ 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
if ($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_id ne $seq_region_id )) {
@@ -490,6 +576,7 @@ sub _objs_from_sth {
$throw_away = $misc_feature_id;
next FEATURE;
}
+
$slice = $dest_slice;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
index 492509618243667bf78e371c0f42826198a3479f..fc31865db88f3f2acfa53944185a7d311e314221 100644
--- a/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
@@ -383,20 +383,105 @@ sub _objs_from_sth {
#
# If a destination slice was provided convert the coords
- # If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($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;
+ 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
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
@@ -404,7 +489,6 @@ sub _objs_from_sth {
next FEATURE;
}
-
$slice = $dest_slice;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
index fa25b1c3d3982c9588188fe8140a528b8bed17f0..dc0802dc229e075a79760be83d2939f3326f9e67 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
@@ -287,26 +287,112 @@ sub _objs_from_sth {
#
# If a destination slice was provided convert the coords
- # If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($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;
- }
- }
+ 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
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_id ne $seq_region_id )) {
next FEATURE;
}
+
$slice = $dest_slice;
}
diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
index 33e8fb51523a361abcbc7366a324e940728cc9e4..148ddc9456d17b56c3af9d1715c13c4142f98800 100644
--- a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
@@ -300,14 +300,71 @@ sub fetch_pairs_by_Slice {
$sth->execute();
$sth->bind_columns( \$tag_id, \$pair_id, \$seq_region_id, \$start, \$end, \$strand, \$analysis_id ,\$tag_count);
while ( $sth->fetch ) {
- #convert into relative slice coordinates
- if($slice->strand == 1) {
+ # convert into relative slice coordinates
+ my $seq_region_len = $slice->seq_region_length();
+
+ if ($slice->strand == 1) { # Positive strand
$start = $start - $slice->start + 1;
- $end = $end - $slice->start + 1;
- }
- else{
- $start = $slice->end - $end + 1;
- $end = $slice->end - $start + 1;
+ $end = $end - $slice->start + 1;
+
+ if ($slice->is_circular()) { # Handle circular chromosomes
+ if ($start > $end) { # Looking at a feature overlapping the chromsome origin
+ if ($end > $slice->start) {
+ # Looking at the region in the beginning of the chromosome
+ $start -= $seq_region_len;
+ }
+
+ if ($end < 0) {
+ $end += $seq_region_len;
+ }
+ } else {
+ if ($slice->start > $slice->end && $end < 0) {
+ # Looking at the region overlapping the chromosome origin and
+ # a feature which is at the beginning of the chromosome
+ $start += $seq_region_len;
+ $end += $seq_region_len;
+ }
+ }
+ } # end if ($dest_slice->is_circular...)
+
+ } else { # Negative strand
+ my ($seq_region_start, $seq_region_end) = ($start, $end);
+ $start = $slice->end - $seq_region_end + 1;
+ $end = $slice->end - $seq_region_start + 1;
+
+ if ($slice->is_circular()) {
+ if ($slice->start > $slice->end) { # slice spans origin or replication
+ if ($seq_region_start >= $slice->start) {
+ $end += $seq_region_len;
+ $start += $seq_region_len
+ if $seq_region_end > $slice->start;
+
+ } elsif ($seq_region_start <= $slice->end) {
+ # do nothing
+ } elsif ($seq_region_end >= $slice->start) {
+ $start += $seq_region_len;
+ $end += $seq_region_len;
+
+ } elsif ($seq_region_end <= $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 <= $slice->end and $seq_region_end >= $slice->start) {
+ # do nothing
+ } elsif ($seq_region_start > $seq_region_end) {
+ if ($seq_region_start <= $slice->end) {
+ $start -= $seq_region_len;
+ } elsif ($seq_region_end >= $slice->start) {
+ $end += $seq_region_len;
+ } else { }
+ }
+ }
+ }
+
$strand *= -1;
}
@@ -375,8 +432,75 @@ sub _fetch {
$seqend = $dest_slice_end - $tmp_seq_region_start + 1;
$strand *= -1;
}
- $slice = $dest_slice;
}
+
+ my $seq_region_len = $dest_slice->seq_region_length();
+
+ if ($dest_slice_strand == 1) { # Positive strand
+ $seqstart = $seqstart - $dest_slice_start + 1;
+ $seqend = $seqend - $dest_slice_start + 1;
+
+ if ($dest_slice->is_circular()) { # Handle cicular chromosomes
+ if ($seqstart > $seqend) { # Looking at a feature overlapping the chromsome origin
+ if ($seqend > $dest_slice_start) {
+ # Looking at the region in the beginning of the chromosome.
+ $seqstart -= $seq_region_len;
+ }
+
+ if ($seqend < 0) {
+ $seqend += $seq_region_len;
+ }
+ } else {
+ if ($dest_slice_start > $dest_slice_end && $seqend < 0) {
+ # Looking at the region overlapping the chromosome origin and
+ # a feature which is at the beginning of the chromosome.
+ $seqstart += $seq_region_len;
+ $seqend += $seq_region_len;
+ }
+ }
+ }
+ } else { # Negative strand
+ my $start = $dest_slice_end - $seqend + 1;
+ my $end = $dest_slice_end - $seqstart + 1;
+
+ if ($dest_slice->is_circular()) {
+ if ($dest_slice_start > $dest_slice_end) {
+ # slice spans origin or replication
+ if ($seqstart >= $dest_slice_start) {
+ $end += $seq_region_len;
+ $start += $seq_region_len
+ if $seqend > $dest_slice_start;
+
+ } elsif ($seqstart <= $dest_slice_end) {
+ # do nothing
+ } elsif ($seqend >= $dest_slice_start) {
+ $start += $seq_region_len;
+ $end += $seq_region_len;
+ } elsif ($seqend <= $dest_slice_end) {
+ $end += $seq_region_len
+ if $end < 0;
+ } elsif ($seqstart > $seqend) {
+ $end += $seq_region_len;
+ } else { }
+ } else {
+ if ($seqstart <= $dest_slice_end and $seqend >= $dest_slice_start) {
+ # do nothing
+ } elsif ($seqstart > $seqend) {
+ if ($seqstart <= $dest_slice_end) {
+ $start -= $seq_region_len;
+ } elsif ($seqend >= $dest_slice_start) {
+ $end += $seq_region_len;
+ } else { }
+ }
+ }
+ }
+
+ $seqstart = $start;
+ $seqend = $end;
+ $strand *= -1;
+ }
+
+ $slice = $dest_slice;
}
push @ditag_features,
diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
index d8698cd55d174ff923f675760feda5297eb851df..b02a36959fb832271ae3f399ad226c41dc1e9f23 100644
--- a/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
@@ -298,21 +298,108 @@ sub _objs_from_sth {
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($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;
- }
+ 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 += $seq_region_len;
+
+ } else {
+
+ }
+ }
+ }
- #throw away features off the end of the requested slice
- if($seq_region_end < 1 || $seq_region_start > $dest_slice_length) {
- next FEATURE;
}
+
+ $seq_region_start = $start;
+ $seq_region_end = $end;
+
+ } ## end else [ if ($dest_slice_strand...)]
+
+ # throw away features off the end of the requested slice
+ if($seq_region_end < 1 || $seq_region_start > $dest_slice_length) {
+ next FEATURE;
}
+
$slice = $dest_slice;
}