From 969ed9757c04af3f001f99c5fa49331f2eee1f1c Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 9 Jul 2003 11:15:46 +0000
Subject: [PATCH] use display_id instead of primary id for xrefs added mRNA to
feature table CDS is now actually CDS when there is UTR pseudogenes dump as
misc_RNA instead of as CDS
---
modules/Bio/EnsEMBL/Utils/SeqDumper.pm | 49 ++++++++++++++++++--------
1 file changed, 34 insertions(+), 15 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/SeqDumper.pm b/modules/Bio/EnsEMBL/Utils/SeqDumper.pm
index dc608e5b0a..557b7f81c4 100644
--- a/modules/Bio/EnsEMBL/Utils/SeqDumper.pm
+++ b/modules/Bio/EnsEMBL/Utils/SeqDumper.pm
@@ -620,22 +620,41 @@ sub _dump_feature_table {
foreach my $gene (@{$gene_slice->get_all_Genes}) {
foreach my $transcript (@{$gene->get_all_Transcripts}) {
my $translation = $transcript->translation;
- $value = $self->features2location($transcript->get_all_Exons);
- $self->write(@ff,'CDS', $value);
- $self->write(@ff,'' , '/gene="'.$gene->stable_id().'"');
- $translation &&
- $self->write(@ff,'', '/protein_id="'.$translation->stable_id().'"');
- $self->write(@ff,''
- ,'/note="transcript_id='.$transcript->stable_id().'"');
-
- foreach my $dbl (@{$transcript->get_all_DBLinks}) {
- $value = '/db_xref="'.$dbl->dbname().':'.$dbl->primary_id().'"';
- $self->write(@ff, '', $value);
- }
- if($translation) {
+
+ # normal transcripts get dumped differently than pseudogenes
+ if($translation) {
+ #normal transcript
+ $value = $self->features2location($transcript->get_all_Exons);
+ $self->write(@ff, 'mRNA', $value);
+ $self->write(@ff,'' , '/gene="'.$gene->stable_id().'"');
+
+ # ...and a CDS section
+ $value =
+ $self->features2location($transcript->get_all_translateable_Exons);
+ $self->write(@ff,'CDS', $value);
+ $self->write(@ff,'' , '/gene="'.$gene->stable_id().'"');
+ $self->write(@ff,'', '/protein_id="'.$translation->stable_id().'"');
+ $self->write(@ff,''
+ ,'/note="transcript_id='.$transcript->stable_id().'"');
+
+ foreach my $dbl (@{$transcript->get_all_DBLinks}) {
+ $value = '/db_xref="'.$dbl->dbname().':'.$dbl->display_id().'"';
+ $self->write(@ff, '', $value);
+ }
+
$value = '/translation="'.$transcript->translate()->seq().'"';
$self->write(@ff, '', $value);
- }
+ } else {
+ #pseudogene
+ $value = $self->features2location($transcript->get_all_Exons);
+ $self->write(@ff, 'misc_RNA', $value);
+ $self->write(@ff,'' , '/gene="'.$gene->stable_id().'"');
+ foreach my $dbl (@{$transcript->get_all_DBLinks}) {
+ $value = '/db_xref="'.$dbl->dbname().':'.$dbl->primary_id().'"';
+ $self->write(@ff, '', $value);
+ }
+ $self->write(@ff,'' , '/note="pseudogene"');
+ }
}
}
@@ -660,7 +679,7 @@ sub _dump_feature_table {
$self->write(@ff, 'mRNA', $self->features2location($exons));
$self->write(@ff, '', '/product="'.$transcript->translate()->seq().'"');
$self->write(@ff, '', '/note="Derived by automated computational' .
- 'analysis using gene prediction method:' .
+ ' analysis using gene prediction method:' .
$transcript->analysis->logic_name . '"');
}
}
--
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