[ensembl-dev] Release 65 - "cigar_line" exception when calling get_SimpleAlign on homology object

[Javier Herrero]

Hi Giuseppe

After some investigation, it would appear that this affects a new type 
of homologies we have added in Ensembl 65. These are relationships 
between the genes on the reference assembly and their matching version 
on the haplotypes and assembly patches (this affect the human genome 
only). Strictly speaking, these are no homologies, but that information 
fits well in that part of the compara schema.

These data are stored as ENSEMBL_PROJECTIONS (this is the 
method_link_type). In the homology object, they are classified as either 
projection_unchanged or projection_altered ($homology->description). To 
resolve your problem, I'd suggest you ignore the projections. This might 
work for you:

next if ($homology->description =~ /^projection/)


We will look into ways to improve this. At the very least, the API 
should not return such error.

Sorry for the inconvenience.

Javier

On 19/01/12 11:27, Giuseppe G. wrote:
> Hi,
>
> I'm on V. 65. and bioperl 1.6.1. The following exception has been 
> reproduced on another machine with Bioperl 1.2.3.
>
> I use some bioperl code called the api to obtain the overall 
> percentage identity of two orthologous sequences
>
> my $pairwise_alignment_from_multiple = $homology->get_SimpleAlign;
> if($pairwise_alignment_from_multiple){
>                     $opi = 
> $pairwise_alignment_from_multiple->overall_percentage_identity;
>                }else{
>                     $opi = '-';
>                }
>
> This worked fine until v.64.
>
> I'm now getting the following exception on some entries:
>
>> -------------------- EXCEPTION --------------------
>> MSG: To get an alignment_string, the cigar_line needs to be define
>>
>> STACK Bio::EnsEMBL::Compara::Attribute::alignment_string 
>> /home/giuseppe/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/Attribute.pm:64
>> STACK Bio::EnsEMBL::Compara::Homology::get_SimpleAlign 
>> /home/giuseppe/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/Homology.pm:208
>> STACK <MYCODE>
>> Ensembl API version = 65
>> ---------------------------------------------------
>
> Any help would be appreciated.
>
> Best,
> Giuseppe
>

-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK