From a012e095dc1a6d3d02e5343ae1445f432626b0ee Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Wed, 31 Jul 2013 10:20:34 +0000
Subject: [PATCH] Added circular slice case for positive/negative strands when
computing slice relative coordinates
---
.../External/ExternalFeatureAdaptor.pm | 85 +++++++++++++++----
1 file changed, 68 insertions(+), 17 deletions(-)
diff --git a/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm b/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
index e83bfd3a63..b19418c0cf 100644
--- a/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
@@ -376,26 +376,77 @@ sub fetch_all_by_Slice {
}
}
- #shift the feature coordinates again if
- #the requested slice is not the full seqregion
- if($slice->start != 1 || $slice->strand != 1) {
- #convert from assembly coords to slice coords
+ # convert from assembly coords to slice coords
+ # handle the circular slice case
+ my $seq_region_len = $slice->seq_region_length();
+ foreach my $f (@out) {
my($f_start, $f_end, $f_strand);
- foreach my $f (@out) {
- if($slice_strand == 1) {
- $f_start = $f->start - $slice_start + 1;
- $f_end = $f->end - $slice_start + 1;
- $f_strand = $f->strand;
- } else {
- $f_start = $slice_end - $f->end + 1;
- $f_end = $slice_end - $f->start + 1;
- $f_strand = $f->strand * -1;
+
+ if ($slice->strand == 1) { # Positive strand
+ $f_start = $f->start - $slice_start + 1;
+ $f_end = $f->end - $slice_start + 1;
+ $f_strand = $f->strand;
+
+ if ($slice->is_circular()) { # Handle cicular chromosomes
+ if ($f_start > $f_end) { # Looking at a feature overlapping the chromsome origin.
+ if ($f_end > $slice_start) {
+ # Looking at the region in the beginning of the chromosome.
+ $f_start -= $seq_region_len;
+ }
+
+ if ($f_end < 0) {
+ $f_end += $seq_region_len;
+ }
+ } else {
+ if ($slice_start > $slice_end && $f_end < 0) {
+ # Looking at the region overlapping the chromosome origin and
+ # a feature which is at the beginning of the chromosome.
+ $f_start += $seq_region_len;
+ $f_end += $seq_region_len;
+ }
+ }
+ }
+ } else { # Negative strand
+ my ($seq_region_start, $seq_region_end) = ($f->start, $f->end);
+ $f_start = $slice_end - $seq_region_end + 1;
+ $f_end = $slice_end - $seq_region_start + 1;
+ $f_strand = $f->strand * -1;
+
+ if ($slice->is_circular()) {
+ if ($slice_start > $slice_end) { # slice spans origin or replication
+ if ($seq_region_start >= $slice_start) {
+ $f_end += $seq_region_len;
+ $f_start += $seq_region_len
+ if $seq_region_end > $slice_start;
+
+ } elsif ($seq_region_start <= $slice_end) {
+ # do nothing
+ } elsif ($seq_region_end >= $slice_start) {
+ $f_start += $seq_region_len;
+ $f_end += $seq_region_len;
+ } elsif ($seq_region_end <= $slice_end) {
+ $f_end += $seq_region_len
+ if $f_end < 0;
+ } elsif ($seq_region_start > $seq_region_end) {
+ $f_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) {
+ $f_start -= $seq_region_len;
+ } elsif ($seq_region_end >= $slice_start) {
+ $f_end += $seq_region_len;
+ } else { }
+ }
+ }
}
-
- $f->start($f_start);
- $f->end($f_end);
- $f->strand($f_strand);
}
+
+ $f->start($f_start);
+ $f->end($f_end);
+ $f->strand($f_strand);
}
return \@out;
--
GitLab