From 4d4bdfa5337a1a5166c135a292ef33ccbd0cfcc4 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Mon, 30 Sep 2013 16:11:17 +0000
Subject: [PATCH] Fixes for the alt alleles code. We needed to make sure we
used the right variables in the code. Also needed to make sure an array is
actually defined during construction
---
misc-scripts/alt_alleles/alt_alleles.pl | 12 +++++++-----
modules/Bio/EnsEMBL/AltAlleleGroup.pm | 2 +-
2 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/alt_alleles/alt_alleles.pl b/misc-scripts/alt_alleles/alt_alleles.pl
index 747e1a611b..df348dc9b5 100644
--- a/misc-scripts/alt_alleles/alt_alleles.pl
+++ b/misc-scripts/alt_alleles/alt_alleles.pl
@@ -99,12 +99,12 @@ my %no_gene_id;
my @new_groups;
foreach my $group (@{$vega_groups}) {
my $members = $group->get_all_Genes_types();
- my $new_core_group = undef;
+ my $new_core_group = Bio::EnsEMBL::AltAlleleGroup->new();
foreach my $member (@{$members}) {
my ($vega_gene, $attribs_hash) = @{$member};
- if(exists $vega_to_ensembl_core_gene_id{$vega_gene->stable_id()}) {
- $new_core_group ||= Bio::EnsEMBL::AltAlleleGroup->new(); # initalise if we don't already have one
- foreach my $gene_id (keys %{$vega_to_ens_id{$vega_stable_id}} ) {
+ my $vega_stable_id = $vega_gene->stable_id();
+ if(exists $vega_to_ensembl_core_gene_id{$vega_stable_id}) {
+ foreach my $gene_id (keys %{$vega_to_ensembl_core_gene_id{$vega_stable_id}} ) {
#Add each gene in. If we had a 1:m relationship then we copy the attribute already assigned
#across
$new_core_group->add_member($gene_id, $attribs_hash);
@@ -115,7 +115,9 @@ foreach my $group (@{$vega_groups}) {
print STDERR "no ensembl gene_id found for vega stable id $vega_stable_id in core\n";
}
}
- push(@new_groups, $new_core_group);
+ if($new_core_group->size() > 0) {
+ push(@new_groups, $new_core_group);
+ }
}
#
diff --git a/modules/Bio/EnsEMBL/AltAlleleGroup.pm b/modules/Bio/EnsEMBL/AltAlleleGroup.pm
index a908141db4..826ad2c184 100644
--- a/modules/Bio/EnsEMBL/AltAlleleGroup.pm
+++ b/modules/Bio/EnsEMBL/AltAlleleGroup.pm
@@ -131,7 +131,7 @@ sub new {
my $self = $class->SUPER::new(@_);
my ( $list ) = rearrange( [ 'MEMBERS'], @_ );
- $self->{'MEMBERS'} = $list;
+ $self->{'MEMBERS'} = $list || [];
return $self;
}
--
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