[ensembl-dev] ensembl genomes 18_71 protein sequences not returned properly

[James Allen]

Hello,
Thanks for bringing this to our attention; the all-N sequences were due to some missing data in one of the databases on the public mysql server. This has been rectified, and the queries should now work.

Thanks,
James


On Mon, 29 Apr 2013 14:11:50 +0200
Moretti Sébastien <sebastien.moretti at unil.ch> wrote:

> Hi
> 
> I would like to extract protein and nucleotide CDS related sequences 
> from Drosophila ensembl gene trees with API 71 on ensembl metazoa 18.
> 
> I get some warnings (see at the bottom of the e-mail) for each tree and 
> get nucleotide sequences that look fine. But all protein sequences look 
> the same, all amino acid letters are N.
> e.g.
>  >FBpp0227954
> ----------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------NNNN
> NNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> 
> 
>  From a tree object, I use $tree->get_SimpleAlign to get the protein 
> MSA, and $tree->get_SimpleAlign(-cdna=>1) for the nucleotide CDS MSA.
> 
> 
> I used the same script last week on Glires taxon on ensembl 71 and 
> everything looked fine.
> 
> 
> Has something changed in the API ?
> 
> 
> Use of uninitialized value $sequence in substr at
>  
> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm 
> line 467 (#1)
> substr outside of string at
>  
> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm 
> line 467 (#2)
> Use of uninitialized value $substring in pattern match (m//) at
>  
> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm 
> line 468 (#1)
> Use of uninitialized value in numeric lt (<) at
>  
> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm 
> line 473 (#1)
> Use of uninitialized value in subtraction (-) at
>  
> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm 
> line 474 (#1)
> 
> 
> Regards
>