[ensembl-dev] REST API Does not return Tarsier sequence in LASTZ_NET

[Reed A. Cartwright]

Through the Perl API you can retrieve a GenomeBlock for Human-Tarsier
LASTZ_NET alignment.  This can be seen in the website.

http://uswest.ensembl.org/Homo_sapiens/Location/Compara_
Alignments?align=699--Tarsius_syrichta--GeneScaffold_12:
55117-149885;db=core;g=ENSG00000003096;r=X:117972731-117972828

I have also confirmed it locally using the latest perl API.

However, the same query via the REST API only returns the human sequence.

http://rest.ensembl.org/alignment/region/homo_sapiens/
X:117972731-117972828:-1/?content-type=application/json;
method=LASTZ_NET;species_set=homo_sapiens;species_set=tarsius_syrichta

Human-Gorilla is also affected.  What is special about Human-Tarsier and
Human-Gorilla is that both are missing branch-length information in the
database.  Looking through the REST API code, I believe the problem is
occurring when the GenomeAlignBlock is being converted to a
GenomicAlignTree here:

https://github.com/Ensembl/ensembl-rest/blob/release/87/lib/EnsEMBL/REST/Model/GenomicAlignment.pm#L113-L125

When I call fetch_all_by_MethodLinkSpeciesSet_Slice using the perl API,
locally, I can see both sequences, so I'm assuming that they are being
dropped afterwards.

--
Reed A. Cartwright, PhD
Barrett Honors Faculty
Assistant Professor of Genomics, Evolution, and Bioinformatics
School of Life Sciences
Human and Comparative Genomics Laboratory
The Biodesign Institute
Arizona State University
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