From 2e0f66a4f1b626b6e8af7ee56185e53088f121cb Mon Sep 17 00:00:00 2001
From: Web Admin <w3adm@sanger.ac.uk>
Date: Thu, 8 Jun 2006 16:08:30 +0000
Subject: [PATCH] first exon phase fix
---
modules/Bio/EnsEMBL/PredictionTranscript.pm | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/PredictionTranscript.pm b/modules/Bio/EnsEMBL/PredictionTranscript.pm
index e543cbed37..14da0b4f16 100644
--- a/modules/Bio/EnsEMBL/PredictionTranscript.pm
+++ b/modules/Bio/EnsEMBL/PredictionTranscript.pm
@@ -262,8 +262,14 @@ sub translation {
# "translation");
}
+ my $Xseq = $self->spliced_seq();
+ my $start_phase = $start_exon->phase;
+ if( $start_phase > 0 ) {
+ $Xseq = "N"x$start_phase . $Xseq;
+ }
+
my $tmpSeq = new Bio::Seq( -id => "dummy",
- -seq => $self->spliced_seq(),
+ -seq => $Xseq,
-moltype => "dna" );
return Bio::EnsEMBL::Translation->new
--
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