From 62bdd49d0c9221d60b86e11efa6fd23d885d7904 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 30 Jun 2011 12:53:09 +0000
Subject: [PATCH] better warning for projections
---
modules/Bio/EnsEMBL/Feature.pm | 39 ++++++++++++++++++++++++++++------
1 file changed, 33 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index 40a14d20b7..669e1ba8a3 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -565,16 +565,23 @@ sub transform {
bless $new_feature, ref $self;
return $new_feature;
}
+ my $projection;
+ if(defined($to_slice)){
+ $projection = $self->project_to_slice( $to_slice ); }
+ else{
+ $projection = $self->project( $cs_name, $cs_version );
+ }
- my $projection = $self->project( $cs_name, $cs_version );
-
+ if(@$projection == 0){
+ return undef;
+ }
if( @$projection != 1 and !defined($to_slice)) {
- # warn "MORE than one projection and NO slice specified ";
- # warn "from ".$self->slice->name." to $cs_name, $cs_version\n";
+# warn "MORE than one projection and NO slice specified ";
+# warn "from ".$self->slice->name." to $cs_name, $cs_version\n";
return undef;
}
my $index = 0;
- if(defined($to_slice) and @$projection != 1 ){
+ if(defined($to_slice)){
my $found = 0;
my $i = 0;
foreach my $proj (@{$projection}) {
@@ -586,7 +593,27 @@ sub transform {
$i++;
}
if(!$found){
- warn "MORE than one projection and none to slice specified\n";
+ if(@$projection != 1){
+ if(@$projection == 0){
+ warn "number of mappings is ".@$projection."\n";
+ warn "could not project feature ".ref($self)." from ".$self->slice->seq_region_name." to ".$to_slice->seq_region_name."\n";
+ warn "In the region of ".$self->slice->start." <-> ".$self->slice->end."\n";
+ warn "feat start=".($self->slice->start+$self->start)."\tend=".($self->slice->start+$self->end)."\n";
+ }
+ else{
+ foreach my $proj (@{$projection}) {
+ my $slice = $proj->[2];
+ warn "available slice ".$slice->seq_regon_name."\n";
+ }
+ warn "MORE than one projection and none to slice specified (".$to_slice->seq_region_name.")\n";
+ }
+ }
+ else {
+ foreach my $proj (@{$projection}) {
+ warn "Mapping is to ".$proj->[2]->seq_region_name."\n";
+ }
+ warn "One projection but none to slice specified\n";
+ }
return undef;
}
}
--
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