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Avert cross species contamination in VEP cache dump #1575

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merged 1 commit into from
Jan 16, 2024
Merged

Avert cross species contamination in VEP cache dump #1575

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88 changes: 39 additions & 49 deletions modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -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(<IN>) {
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(<IN>) {
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(<IN>) {
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(<IN>) {
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;
}


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