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

[Giuseppe G.]

Thank you Javier will let you know how it goes.

Giuseppe

On 19/01/12 17:01, Javier Herrero wrote:
> 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
>>
>

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