[ensembl-dev] Problem with AlignSlice from GenomicAlignBlock

[Kathryn Beal]

Hi Marc,
I think I've fixed the bug. You will need to check out a new version of the compara API (HEAD code). The
problem was in the ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignSlice.pm module.

Cheers
Kathryn

> Hi,
> 
> so I have been trying to create AlignSlices from GenomicAlignBlocks using
> 
> my $align_slice_adaptor =
>     Bio::EnsEMBL::Registry->get_adaptor("Multi", "compara", "AlignSlice");
> 
> my $align_slice =
>     $align_slice_adaptor->fetch_by_GenomicAlignBlock($this_block);
> 
> However, I receive the following error message
> 
> MSG: 7 arguments expected
> STACK Bio::EnsEMBL::Mapper::add_map_coordinates /home/mh/ensembl/src/ensembl/modules/Bio/EnsEMBL/Mapper.pm:542
> STACK Bio::EnsEMBL::Compara::GenomicAlign::get_Mapper
> /home/mh/ensembl/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomicAlign.pm:1489
> STACK Bio::EnsEMBL::Compara::AlignSlice::_create_underlying_Slices
> /home/mh/ensembl/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignSlice.pm:938
> STACK Bio::EnsEMBL::Compara::AlignSlice::new
> /home/mh/ensembl/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignSlice.pm:318
> STACK Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::fetch_by_GenomicAlignBlock
> /home/mh/ensembl/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/AlignSliceAdaptor.pm:314
> STACK toplevel /home/mh/scripts/ensembl_align_slice.pl:127
> Ensembl API version = 63
> 
> Everything up to that point should be fine (I can call functions on the genomic_align_block object like
> '->length') - so I am not sure what's wrong there.
> 
> I use Ubuntu 11.04 server and tried both a local installation of ensembl_compara_63 as well as remote, if that
> mattes at all. The datasets I tried were the 19 vertebrate PECAN alignment as well as BLASTZ_NET for human and
> chimp. The error occurred both with my 1month old install of the api as well is with the version currently
> hosted on the ftp server.
> 
> /Marc
> 
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-- 
Dr Kathryn Beal
EnsEMBL
EMBL-European Bioinformatics Institute       Tel. +44 (0)1223 494458
Wellcome Trust Genome Campus, Hinxton        Fax. +44 (0)1223 494468
Cambridge CB10 1SD, UK