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

[Moretti Sébastien]

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

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/