[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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