From 9affb7d397cfaed206fb67f184916359fec60e1e Mon Sep 17 00:00:00 2001
From: Yuan Chen <yuan@sanger.ac.uk>
Date: Fri, 10 Oct 2008 16:15:35 +0000
Subject: [PATCH] update to add consequence_type of within_mature_miRNA
---
.../Bio/EnsEMBL/Utils/TranscriptAlleles.pm | 32 +++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
index f6f6cb3154..f2de3cb336 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
@@ -284,6 +284,38 @@ sub type_variation {
return [];
}
+ if (!$tr->translation()) {#for other biotype rather than coding/IG genes
+ # check if the variation is completely outside the transcript:
+
+ if($var->end < $tr->start()) {
+ $var->type( ($tr->strand() == 1) ? 'UPSTREAM' : 'DOWNSTREAM' );
+ return [$var];
+ }
+ if($var->start > $tr->end()) {
+ $var->type( ($tr->strand() == 1) ? 'DOWNSTREAM' : 'UPSTREAM' );
+ return [$var];
+ }
+ if ($var->start >= $tr->start() and $var->end <= $tr->end()) {#within the transcript
+ if ($tr->biotype() eq "miRNA") {
+ my ($attribute) = @{$tr->get_all_Attributes('miRNA')};
+ #the value is the mature miRNA coordinate within miRNA transcript
+ if ( $attribute->value =~ /(\d+)-(\d+)/ ) {
+ @mapper_objs = $trans->cdna2genomic($1, $2, $tr->strand);#transfer cdna value to genomic coordinates
+ foreach my $obj ( @mapper_objs ){#Note you can get more than one mature seq per miRNA
+ if( $obj->isa("Bio::EnsEMBL::Mapper::Coordinate")){
+ if ($var->start >= $obj->start() and $var->end <= $obj->end()) {
+ $var->type("WITHIN_MATURE_miRNA");
+ $return [$var];
+ }
+ }
+ }
+ }
+ }
+ $var->type("WITHIN_NON_CODING_GENE");
+ return [$var];
+ }
+ }
+
my $tm = $tr->get_TranscriptMapper();
my @coords = $tm->genomic2cdna($var->start,
$var->end,
--
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