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

[Will McLaren]

Hi Stuart,

Apologies, I tweaked this bit of code for v75 and made a typo which causes
this error.

I've fixed up the code on GitHub - if you re-download the VEP archive or
git pull in the ensembl-tools directory (if you used git to get it) you
should get the fixed version.

You could also just download this file over the top of your existing
variant_effect_predictor.pl script:

https://github.com/Ensembl/ensembl-tools/blob/release/75/scripts/variant_effect_predictor/variant_effect_predictor.pl

Regards

Will McLaren
Ensembl Variation


On 31 March 2014 17:04, Stuart Watt <Stuart.Watt at oicr.on.ca> wrote:

>  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
> 661 University Avenue
> Suite 510
> Toronto, Ontario
> Canada M5G 0A3
>
> Tel: 647-260-7990
> Twitter: @morungos
> Toll-free: 1-866-678-6427
>
> www.oicr.on.ca
>
> This message and any attachments may contain confidential and/or
> privileged information for the sole use of the intended recipient. Any
> review or distribution by anyone other than the person for whom it was
> originally intended is strictly prohibited. If you have received this
> message in error, please contact the sender and delete all copies.
> Opinions, conclusions or other information contained in this message may
> not be that of the organization.
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140401/e794d39e/attachment.html>