[ensembl-dev] $protein_tree_adaptor->fetch_all_roots

[Matthieu Muffato]

Hi Sébastien

I also have the same warning on my computer, but have never seen any 
problem in the output. I assume it happens because I am not using 
BioPerl 1.2.3 but a more recent version, but I've never looked into 
that. Do you see this warning only for the most recent releases ? or has 
it been around for a while ?

Best,
Matthieu

On 11/01/12 11:19, Sébastien Moretti wrote:
> Hi Matthieu
>
> get_tagvalue works now after adding the
> ensembl_compara_65.protein_tree_attr table.
> Thanks
>
>
> Also while extracting trees and related MSAs I get sometimes this kind
> of message:
> --------------------- WARNING ---------------------
> MSG: In sequence ENSOANP00000021545 residue count gives end value 390.
> Overriding value [3051] with value 390 for Bio::LocatableSeq::end().
>
> I guess this is harmless, isn't it ?
> What does it mean exactly ?
>
> Best regards
> Sébastien
>
>> We have indeed added a new table: protein_tree_attr :) It is used to
>> store all the tags that are actually present in every node.
>>
>> BTW, this will change again in e66, as we will merge the protein trees
>> and the ncRNA trees in a single set of tables
>>
>> Regards,
>> Matthieu
>>
>> On 10/01/12 16:32, Moretti Sébastien wrote:
>>> Using your db, I got
>>> 8 Euteleostomi
>>> the normal behavior I guess.
>>>
>>>
>>> With our ensembl db, I got
>>> 8 MISSING
>>>
>>>
>>> We use truncated db to save some space. I guess some tables are missing
>>> compared to what we used for ensembl 61.
>>> I will try with a full installation.
>>>
>>> Here are tables we load:
>>> - species core db
>>> *_core_*.sql.gz
>>> assembly.*
>>> coord_system.*
>>> dna.*
>>> exon*
>>> meta*
>>> seq_region.*
>>> transcript.*
>>> transcript_stable_id.*
>>> translation.*
>>> translation_stable_id.*
>>>
>>> - compara db
>>> ensembl_compara_*.sql.gz
>>> genome_db.*
>>> member.*
>>> meta.*
>>> ncbi_taxa_name.*
>>> ncbi_taxa_node.*
>>> protein_tree_member.*
>>> protein_tree_member_score.*
>>> protein_tree_node.*
>>> protein_tree_stable_id.*
>>> protein_tree_tag.*
>>> sequence.*
>>> subset_member.*
>>>
>>> Thanks
>


-- 
Matthieu Muffato, Ph.D.
Ensembl Developer - Comparative Genomics
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom