[ensembl-dev] $protein_tree_adaptor->fetch_all_roots

[Moretti Sébastien]

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

> Hi Sébastien
>
> The following code is working for me, and prints the taxon name of the
> tree starting at node_id=8 (also works with 248).
>
> my $tree = $protein_tree_adaptor->fetch_node_by_node_id(8);
> my $tax_level = $tree->get_tagvalue('taxon_name');
> print $tree->node_id, " ", (defined $tax_level ? $tax_level :
> "MISSING"), "\n";
>
> Is it working for you as well ? If so, the error must be a side effect
> of another part of your script. Could you then attach it ? (at least its
> beginning)
>
> Thank you,
> Matthieu
>
> On 10/01/12 15:48, Moretti Sébastien wrote:
>>> Hi Sébastien
>>>
>>> There was indeed some work on tags in rel 65, but this should be
>>> transparent for users.
>>> However, missing tags are now returning "undef" instead of an empty
>>> string. Does it match your error ?
>>
>> I have always tested $tax_level this way:
>> if ( defined $tax_level && $tax_level ne '' ){ ... }
>>
>> Currently the script does not go into this if statement.
>>
>>> That said, every internal node should have a 'taxon_name' tag, and
>>> leaves shouldn't (same behaviour as in rel 64). Can you give me an
>>> example of a failing $node_id ?
>>
>> Here are 2 failing node_id
>> 8 (for ENSGT00470000042273)
>> 248 (for ENSGT00530000064177)
>>
>>
>> Sébastien

-- 
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/