[ensembl-dev] VEP offline won't work with --sift/--polyphen

[Stuart Watt]

Has something changed with the VEP options for —sift and —polyp hen when run offline?

I’m getting "INFO: --sift is not available for this species” message (same for polyphen) when I use it.

Culpable lines appear to be (from #1833):

  my $string = 'config_'.$tool.'_version';
  if(!defined($config->{$string}) && !defined($config->{offline})) {
    my $var_mca = $config->{reg}->get_adaptor($config->{species}, 'variation', 'metacontainer');
    my $values = $var_mca->list_value_by_key($tool.'_version') if defined($var_mca);
    $config->{$string} = $values->[0] if $values && scalar @$values;
  }

  if(!defined($config->{$string})) {
    debug("INFO: --$tool is not available for this species") unless defined($config->{quiet});
    delete $config->{$tool};
  }

Because $config->{config_sift_version} is never set anywhere, this simply falls through the first condition into the second, removing the setting.

When ran this in the debugger and manually set $config->{config_sift_version} and $config->{config_polyphen_version} , all seemed to work fine. It seems they should either be set somehow, or be not required. Or maybe the first condition is supposed to test for defined($config->{$tool}) instead.

I don’t know the innards of the config setup here, but any advice would be welcome.

All the best
Stuart

--

Stuart Watt, PhD

Scientific Associate

Ontario Institute for Cancer Research

MaRS Centre
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