[ensembl-dev] get_SimpleAlign problem with cdna

[Moretti Sébastien]

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

-- 
Sébastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://myhits.vital-it.ch/