Comments (4)
My options are:
A) use a global setting to switch from join
to outer join
.
B) customize the individual joins defined in the table specifying the joins (i.e. the .JOINS
table).
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Use cases:
- use
transcripts
to fetch all transcripts of a gene and add (if available) protein annotation: in this case we want to get all transcripts, also the non-coding ones. ->outer join
. - get all genes with a certain protein domain. In this case we use
genes
with aProtdomidFilter
thus it should work with both types of joins. - use a
proteins
method to get all proteins and add e.g.gene_name
as a column. In this case we don't want an outer join that joins the /tx/ and /protein/ tables. ->join
.
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The only solution to solve point 3 above and don't run into an issue when joining the protein and uniprot tables (not every protein id is annotated to an uniprot id) is to use left outer join
and specify the table from which the join should start (i.e. gene for genes
, protein for proteins
etc).
from ensembldb.
This ends up in implementing a new join engine.
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