[ensembl-dev] api v60 to v62

Graham Ritchie grsr at ebi.ac.uk
Fri Jun 24 16:31:57 BST 2011


Hi Stef,

This part of the variation API changed quite a lot under the hood for v62, and we did try to maintain the same interface, but you may have found somewhere where the interface has changed. If you could send me a copy of the script, or even just a minimal script that exhibits the same bug, I will be able to try to establish the problem much more quickly.

Cheers,

Graham


On 24 Jun 2011, at 15:23, mailsvl at fastmail.fm wrote:

> Hi everyone,
> 
> We have a script based on ensembl api v60 (where it works without
> errors) and it almost runs flawless with v62 as well except for one
> error:
> 
> Can't call method "display_term" on an undefined value at
> /data/common_modules/ensembl62/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeatureOverlap.pm
> line 530.
> 
> If I remove this call/line everything runs fine:
> 
> $consequence = $transcript_variation->display_consequence if defined
> $transcript_variation->display_consequence;
> 
> ...but then I'm left without the consequences so thats not really an
> option ;) Anyone knows what change from v60 to v62 makes this method now
> run into problems?
> 
> Thanks!
> Stef
> __________________
> http://www.fastmail.fm
> 
> 
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