[ensembl-dev] get_SimpleAlign problem with cdna

[Matthieu Muffato]

Hi Sébastien

Your initial way of sorting trees by stable_id is actually ok.

Can you add the "-clusterset_id => 'default'" to the fetch_all() call ?
On top of the default, usual, gene trees, we now store the other trees 
computed by TreeBest (phyml, neighbour-joining) and fetch_all() returns 
all of them

Regards,
Matthieu

On 16/08/12 08:40, Moretti Sébastien wrote:
> Hi Matthieu
>
> It works without warnings now, thanks.
>
>
>
> I have another question related to API 68.
> With API 67 I tried to order genetrees to always get the same parsing
> order:
>
> my $tree_adaptor = $reg->get_adaptor('Multi', 'compara', 'GeneTree');
> my @children = @{$tree_adaptor->fetch_all(-tree_type => 'tree',
> -member_type => 'protein')};
>
> for my $tree ( sort {$a->stable_id cmp $b->stable_id} (@children) ){
>      ....
> }
>
>
>
> With API 68 I get this warning:
> Use of uninitialized value in string comparison (cmp)
>
> $a->root->stable_id does not seem to work.
> So, I tried this
> for my $tree (sort {$a->root->node_id  <=>  $b->root->node_id}
> (@children)) {
>      ....
> }
>
> it looks to work to order things but it is really much slower, and order
> by internal id, not stable_id.
>
>
> Do you have any idea how to order by genetree stable_id with API 68 ?
>
> Regards
> Sébastien
>
>> Hi Sébastien
>>
>> I have also just noticed this warning too. You can ignore it: the
>> alignment is still correct.
>>
>> I have patched the HEAD and branch-68 files on the CVS. You can update
>> ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm and the
>> script should not display that warning any more.
>>
>> Regards,
>> Matthieu
>


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