I am trying to run VEP using the plugin FATHMM-MKL. However, it is generating an error:
WARNING: Failed to compile plugin FATHMM_MKL: Global symbol "$allele" requires explicit package name (did you forget to declare "my $allele"?) at FATHMM_MKL.pm line 92.
Global symbol "$allele" requires explicit package name (did you forget to declare "my $allele"?) at FATHMM_MKL.pm line 93.
Global symbol "$allele" requires explicit package name (did you forget to declare "my $allele"?) at FATHMM_MKL.pm line 94.
Compilation failed in require at (eval 63) line 2.
BEGIN failed--compilation aborted at (eval 63) line 2.
I managed to avoid the error by editing the FATHMM_MKL.pm file, specifically the sub run,
adding my to foreach my $allele (@{$alleles}) {:
sub run {
my ($self, $tva) = @_;
my $vf = $tva->variation_feature;
return {} unless $vf->{start} == $vf->{end};
# get allele, reverse comp if needed
my $alleles = $tva->base_variation_feature->alt_alleles;
# adjust coords, file is BED-like (but not 0-indexed, go figure...)
my ($s, $e) = ($vf->{start}, $vf->{end} + 1);
foreach my $data(@{$self->get_data($vf->{chr}, $s, $e)}) {
foreach my $allele (@{$alleles}) {
reverse_comp(\$allele) if $vf->{strand} < 0;
if($data->{start} == $s && $allele eq $data->{alt}) {
return $data->{result};
}
}
}
return {};
}
Hi @JasperBoom,
Thank you for reporting the issue.
We will include a fix in the next release, in the meantime, you should use your local version of the file.
Greetings!
I am trying to run VEP using the plugin FATHMM-MKL. However, it is generating an error:
I managed to avoid the error by editing the FATHMM_MKL.pm file, specifically the
sub run
, addingmy
toforeach my $allele (@{$alleles}) {
: