[ensembl-dev] $protein_tree_adaptor->fetch_all_roots

[Sébastien Moretti]

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

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