Debugged handling of negative strand slices on circular chromosomes

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -646,6 +646,8 @@ FEATURE: while ( $sth->fetch() ) {
     # If a destination slice was provided convert the coords.
     #
     if ( defined($dest_slice) ) {
+      my $seq_region_len = $dest_slice->seq_region_length();
+
       if ( $dest_slice_strand == 1 ) {
         # On the positive strand.
 
@@ -685,58 +687,63 @@ FEATURE: while ( $sth->fetch() ) {
       } else {
         # On the negative strand.
 
-        if ( $seq_region_start > $seq_region_end && $dest_slice->is_circular() )
-        {
-          # Handle circular chromosomes.
+	my $start = $dest_slice_end - $seq_region_end + 1;
+	my $end = $dest_slice_end - $seq_region_start + 1;
 
-          if ( $dest_slice_start > $dest_slice_end ) {
-            my $tmp_seq_region_start = $seq_region_start;
-            $seq_region_start = $dest_slice_end - $seq_region_end + 1;
-            $seq_region_end =
-              $dest_slice_end +
-              $dest_slice->seq_region_length() -
-              $tmp_seq_region_start + 1;
-          } else {
+	if ($dest_slice->is_circular()) {
 
-            if ( $seq_region_end > $dest_slice_start ) {
-              # Looking at the region in the beginning of the
-              # chromosome.
-              $seq_region_start = $dest_slice_end - $seq_region_end + 1;
-              $seq_region_end =
-                $seq_region_end -
-                $dest_slice->seq_region_length() -
-                $dest_slice_start + 1;
-            } else {
-              my $tmp_seq_region_start = $seq_region_start;
-              $seq_region_start =
-                $dest_slice_end -
-                $seq_region_end -
-                $dest_slice->seq_region_length() + 1;
-              $seq_region_end =
-                $dest_slice_end - $tmp_seq_region_start + 1;
-            }
+	  if ($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;
 
-        } else {
-          # Non-circular chromosome.
+	    } elsif ($seq_region_start <= $dest_slice_end) {
+	      # do nothing
+	    } elsif ($seq_region_end >= $dest_slice_start) {
+	      $start += $seq_region_len;
+	      $end += $seq_region_len;
 
-          my $tmp_seq_region_start = $seq_region_start;
-          $seq_region_start = $dest_slice_end - $seq_region_end + 1;
-          $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
-        }
+	    } elsif ($seq_region_end <= $dest_slice_end) {
 
-        $seq_region_strand = -$seq_region_strand;
+	      $end += $seq_region_len
+		if $end < 0;
 
-      } ## end else [ if ( $dest_slice_strand...)]
+	    } elsif ($seq_region_start > $seq_region_end) {
+		  
+	      $end += $seq_region_len;
 
-      # 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 != $seq_region_id ) )
-      {
-        next FEATURE;
-      }
+	    } else {
+		  
+	    }
+      
+	  } else {
+
+	    if ($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...)]
 
       $slice = $dest_slice;
     } ## end if ( defined($dest_slice...))

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -1607,9 +1607,10 @@ FEATURE: while ($sth->fetch()) {
 	# If a destination slice was provided convert the coords.
 	#
 	if (defined($dest_slice)) {
-	  if ($dest_slice_strand == 1) {
-		# Positive 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;
 
@@ -1620,13 +1621,14 @@ FEATURE: while ($sth->fetch()) {
 			# 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 -= $dest_slice->seq_region_length();
+			  $seq_region_start -= $seq_region_len;
 			}
 
 			if ($seq_region_end < 0) {
-			  $seq_region_end += $dest_slice->seq_region_length();
+			  $seq_region_end += $seq_region_len;
 			}
 
 		  } else {
@@ -1637,53 +1639,72 @@ FEATURE: while ($sth->fetch()) {
 			  # Looking at the region overlapping the chromosome
 			  # origin and a feature which is at the beginning of the
 			  # chromosome.
-			  $seq_region_start += $dest_slice->seq_region_length();
-			  $seq_region_end   += $dest_slice->seq_region_length();
+			  $seq_region_start += $seq_region_len;
+			  $seq_region_end   += $seq_region_len;
 			}
 		  }
 
 		} ## end if ($dest_slice->is_circular...)
 
-	  } else {
-		# Negative strand.
+	  } else { # Negative strand
 
-		if (   $dest_slice->is_circular()
-			&& $seq_region_start > $seq_region_end)
-		{
-		  # Handle cicular chromosomes.
+	    my $start = $dest_slice_end - $seq_region_end + 1;
+	    my $end = $dest_slice_end - $seq_region_start + 1;
 
-		  if ($seq_region_end > $dest_slice_start) {
-			# Looking at the region in the beginning of the
-			# chromosome.
-			$seq_region_start = $dest_slice_end - $seq_region_end + 1;
-			$seq_region_end   = $seq_region_end - $dest_slice->seq_region_length - $dest_slice_start + 1;
-		  } else {
-			my $tmp_seq_region_start = $seq_region_start;
-			$seq_region_start = $dest_slice_end - $seq_region_end - $dest_slice->seq_region_length + 1;
-			$seq_region_end   = $dest_slice_end - $tmp_seq_region_start + 1;
-		  }
+	    if ($dest_slice->is_circular()) {
 
-		} else {
-		  # Non-circular chromosome.
+	      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;
 
-		  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;
+		} else {
+		  
 		}
+      
+	      } else {
 
-		$seq_region_strand = -$seq_region_strand;
+		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;
 
-	  } ## end else [ if ($dest_slice_strand...)]
+		  } elsif ($seq_region_end >= $dest_slice_start) {
+		    $end += $seq_region_len;
+
+		  } else {
+		    
+		  }
+		}
+	      }
 
-	  # 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;
-	  }
+	    $seq_region_start = $start;
+	    $seq_region_end = $end;
+	    $seq_region_strand *= -1;
+
+	  } ## end else [ if ($dest_slice_strand...)]
 
 	  $slice = $dest_slice;
 	} ## end if (defined($dest_slice...))

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -1606,6 +1606,8 @@ sub _objs_from_sth {
     # If a destination slice was provided convert the coords.
     #
     if (defined($dest_slice)) {
+      my $seq_region_len = $dest_slice->seq_region_length();
+
       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;
@@ -1633,42 +1635,63 @@ sub _objs_from_sth {
           }
         }
       } else {
-        if (    $dest_slice->is_circular()
-             && $seq_region_start > $seq_region_end )
-        {
-          if ( $seq_region_end > $dest_slice_start ) {
-            # Looking at the region in the beginning of the chromosome.
-            $seq_region_start = $dest_slice_end - $seq_region_end + 1;
-            $seq_region_end =
-              $seq_region_end -
-              $dest_slice->seq_region_length() -
-              $dest_slice_start + 1;
-          } else {
-            my $tmp_seq_region_start = $seq_region_start;
-            $seq_region_start =
-              $dest_slice_end -
-              $seq_region_end -
-              $dest_slice->seq_region_length() + 1;
-            $seq_region_end =
-              $dest_slice_end - $tmp_seq_region_start + 1;
-          }
+	my $start = $dest_slice_end - $seq_region_end + 1;
+	my $end = $dest_slice_end - $seq_region_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 - $tmp_seq_region_start + 1;
-        }
+	if ($dest_slice->is_circular()) {
 
-        $seq_region_strand = -$seq_region_strand;
-      } ## end else [ if ( $dest_slice_strand...)]
+	  if ($dest_slice_start > $dest_slice_end) { 
+	    # slice spans origin or replication
 
-      # 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 $seq_region_id ) )
-      {
-        next FEATURE;
-      }
+	    if ($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...)]
 
       $slice = $dest_slice;
     }