diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm index 27d362716..3178c1439 100644 --- a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm +++ b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm @@ -429,68 +429,58 @@ sub pubmed { my $self = shift; my $as = shift; - if(!exists($self->{_pubmed})) { - - my %pm; - my $file = sprintf( - '%s/pubmed_%s_%s_%s.txt', - $self->required_param('pipeline_dir'), - $self->required_param('species'), - $self->required_param('ensembl_release'), - $self->required_param('assembly') - ); - - if(-e $file) { - open IN, $file or die "Could not write to pubmed file $file $!"; - while() { - chomp; - my @split = split; - $pm{$split[0]} = $split[1]; - } - close IN; - } - else{ - $self->warning('Unable to find PUBMED file: ' . $file); + my %pm; + my $file = sprintf( + '%s/pubmed_%s_%s_%s.txt', + $self->required_param('pipeline_dir'), + $self->required_param('species'), + $self->required_param('ensembl_release'), + $self->required_param('assembly') + ); + + if(-e $file) { + open IN, $file or die "Could not write to pubmed file $file $!"; + while() { + chomp; + my @split = split; + $pm{$split[0]} = $split[1]; } - - $self->{_pubmed} = \%pm; + close IN; + } + else{ + $self->warning('Unable to find PUBMED file: ' . $file); } - return $self->{_pubmed}; + return \%pm; } sub var_synonyms { my $self = shift; my $as = shift; - if(!exists($self->{_var_synonyms})) { - - my %pm; - my $file = sprintf( - '%s/var_synonyms_%s_%s_%s.txt', - $self->required_param('pipeline_dir'), - $self->required_param('species'), - $self->required_param('ensembl_release'), - $self->required_param('assembly') - ); + my %pm; + my $file = sprintf( + '%s/var_synonyms_%s_%s_%s.txt', + $self->required_param('pipeline_dir'), + $self->required_param('species'), + $self->required_param('ensembl_release'), + $self->required_param('assembly') + ); - if(-e $file) { - open IN, $file or die "Could not write to var synonyms file $file $!"; - while() { - chomp; - my @split = split(/\t/); - $pm{$split[0]} = $split[1]; - } - close IN; + if(-e $file) { + open IN, $file or die "Could not write to var synonyms file $file $!"; + while() { + chomp; + my @split = split(/\t/); + $pm{$split[0]} = $split[1]; } - else{ - $self->warning('Unable to find Variation Synonyms file: ' . $file); - } - - $self->{_var_synonyms} = \%pm; + close IN; + } + else{ + $self->warning('Unable to find Variation Synonyms file: ' . $file); } - return $self->{_var_synonyms}; + return \%pm; }