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

Giuseppe G. G.Gallone at sms.ed.ac.uk
Thu Jan 19 11:27:17 GMT 2012


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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