[ensembl-dev] Problem with genome ailgnments, AlignSlice::Slice objects and Alternative assemblies

[Marc P. Hoeppner]

Dear EnsEMBL devs,

I am currently stuck and was hoping for some insights into specifically 
the AlignSlice::Slice objects.

SHORT VERSION:

-------------

When running "get_all_AssemblyExceptionFeatures ()" on an 
AlignSlice::Slice object, I get:

"MSG: Cannot get a AssemblyExceptionFeature adaptor without a 
SliceAdaptor attached to this instance of 
Bio::EnsEMBL::Compara::AlignSlice::Slice"

How do I attach a Slice adaptor to an AlignSlice::Slice object?


LONG VERSION:

-------------

What am I trying to do?

Iterate over whole-genome alignments (pairwise or multi), look for 
annotated features and determine whether they are present in the other 
species of a method_link_species_set using AlignSlice and 
AlignSlice::Slice objects.

What's the problem?

Since some genome assemblies now include ALT regions, the standard 
schema of genome alignments seems to break down a bit (case in point 
LASTZ_NET). For example, a gene on the REF assembly in human aligns to a 
gene in the ALT assembly of mouse, and the REF gene in mouse aligns to 
an ALT locus in human. What this does it confuse my more simplistic 
logic of whether any given locus in species X has a syntenic locus in 
species Y (basically, the counts get inflated when including ALT 
assemblies and I am not getting the sort of 1-to-1 correspondence I am 
looking for).

What have I tried?

For any given REF locus in human, check the AlignSlice::Slice in the 
aligned species and collect all possible ALT assemblies for that 
AlignSlice::Slice. That way I am hoping to reduce they many-to-many 
locus correspondence to a neat, flat 1-to-1.

What's not working?

When I use "get_all_AssemblyExceptionFeatures ()" on an 
AlignSlice::Slice object, I get an unhelpful:

MSG: Cannot get a AssemblyExceptionFeature adaptor without a 
SliceAdaptor attached to this instance of 
Bio::EnsEMBL::Compara::AlignSlice::Slice
FILE: Bio/EnsEMBL/Slice.pm LINE: 1768
CALLED BY: Bio/EnsEMBL/Slice.pm  LINE: 1735
Date (localtime)    = Tue Dec 20 11:32:25 2016
Ensembl API version = 83

Not sure how I attached an adaptor to a Compara object...any helpwould 
be appreciated.

Kind regards,

Marc