From 893438b2906a66f1e16a135623061550f529b7c3 Mon Sep 17 00:00:00 2001
From: Web Admin <w3adm@sanger.ac.uk>
Date: Mon, 15 Dec 2003 10:51:25 +0000
Subject: [PATCH] Added %age context on Gene based slices, tweaks to stable id
fetches, and white space removal
---
modules/Bio/EnsEMBL/ArchiveStableId.pm | 9 ++++++++-
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 7 +++++--
modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm | 2 --
modules/Bio/EnsEMBL/Transcript.pm | 1 -
4 files changed, 13 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/ArchiveStableId.pm b/modules/Bio/EnsEMBL/ArchiveStableId.pm
index ed3d242f7d..df577f48b7 100644
--- a/modules/Bio/EnsEMBL/ArchiveStableId.pm
+++ b/modules/Bio/EnsEMBL/ArchiveStableId.pm
@@ -222,7 +222,14 @@ sub get_translation_archive_id {
my $self = shift;
if( $self->type() eq "Transcript" ) {
- return $self->adaptor->fetch_by_transcript_archive_id( $self );
+ return [$self->adaptor->fetch_by_transcript_archive_id( $self )];
+ } elsif( $self->type() eq "Gene" ) {
+ my $transcripts = $self->adaptor->fetch_all_by_gene_archive_id( $self );
+ my @peptides ;
+ for (@$transcripts) {
+ push @peptides , $self->adaptor->fetch_by_transcript_archive_id( $_ );
+ }
+ return \@peptides;
} else {
return undef;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index d7ab091868..0dfd888126 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -468,10 +468,13 @@ sub fetch_by_gene_stable_id{
if( !defined $geneid ) {
$self->throw("Must have gene id to fetch Slice of gene");
}
- if( !defined $size ) {$size=0;}
-
my ($chr_name,$start,$end) = $self->_get_chr_start_end_of_gene($geneid);
+ if( $size =~/([\d+\.]+)%/ ) {
+ $size = int($1/100 * ($end-$start+1));
+ }
+ if( !defined $size ) {$size=0;}
+
if( !defined $start ) {
my $type = $self->db->assembly_type()
or $self->throw("No assembly type defined");
diff --git a/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm b/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
index a0d462c26e..683ed639ee 100644
--- a/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
@@ -71,8 +71,6 @@ sub new {
return $self;
}
-
-
=head2 fetch_all_by_gene_id_list
Arg [1] : arrayref $gene_ids
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index e569c839c6..bccaf7b389 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -895,7 +895,6 @@ sub get_all_peptide_variations {
return \%out;
}
-
=head2 get_all_SNPs
Arg [1] : (optional) int $flanking
--
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