feat: support for all secondary species#1250

Merged

ejmolinelli merged 24 commits intomainfrom ejmolinelli/secondary-species

Feb 7, 2025

+136-19

Commits on Feb 7, 2025

macaque gene references added

Evan Molinelli
authored and
Evan Molinelli
committed
gencode file updates

Evan Molinelli
authored and
Evan Molinelli
committed
updated gene annotation files from latest gene-processings tep

Evan Molinelli
authored and
Evan Molinelli
committed
enumerate included species; hardcode test resolution to collision-resolved feature_name

Evan Molinelli
authored and
Evan Molinelli
committed
update organism restriction from metazoan descendant to enumerated

Evan Molinelli
authored and
Evan Molinelli
committed
updated h5ad file to use only valid species

Evan Molinelli
authored and
Evan Molinelli
committed
gene references for oryctolagus_cuniculus i.e. european rabbit

Evan Molinelli
authored and
Evan Molinelli
committed
oryctolagus cuniculus - european rabbit

Evan Molinelli
authored and
Evan Molinelli
committed
callithrix jacchus - marmoset

Evan Molinelli
authored and
Evan Molinelli
committed
gorilla gorilla - gorilla

Evan Molinelli
authored and
Evan Molinelli
committed
macaca mulatta - rhesus macaque

Evan Molinelli
authored and
Evan Molinelli
committed
pan troglodytes

Evan Molinelli
authored and
Evan Molinelli
committed
sus scrofa (wild boar) & microcebus murinus (lemur)

Evan Molinelli
authored and
Evan Molinelli
committed
rattus norvegiucs

Evan Molinelli
authored and
Evan Molinelli
committed
lint checks

Evan Molinelli
authored and
Evan Molinelli
committed
explicit gene-id/symbol checks for additional species

Evan Molinelli
authored and
Evan Molinelli
committed
slightly generalized test-gene-bump-dry-run

Evan Molinelli
authored and
Evan Molinelli
committed
fix set over enum

Evan Molinelli
authored and
Evan Molinelli
committed
lint

Evan Molinelli
authored and
Evan Molinelli
committed
speed up tests by putting ontology query behind lru cache

Evan Molinelli
authored and
Evan Molinelli
committed
support some subspecies

Evan Molinelli
authored and
Evan Molinelli
committed
gencode infer species by gene prefix

Evan Molinelli
authored and
Evan Molinelli
committed
lint

Evan Molinelli
authored and
Evan Molinelli
committed
lint check

Evan Molinelli
authored and
Evan Molinelli
committed

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feat: support for all secondary species#1250

Commits on Feb 7, 2025

macaque gene references added

gencode file updates

updated gene annotation files from latest gene-processings tep

enumerate included species; hardcode test resolution to collision-resolved feature_name

update organism restriction from metazoan descendant to enumerated

updated h5ad file to use only valid species

gene references for oryctolagus_cuniculus i.e. european rabbit

oryctolagus cuniculus - european rabbit

callithrix jacchus - marmoset

gorilla gorilla - gorilla

macaca mulatta - rhesus macaque

pan troglodytes

sus scrofa (wild boar) & microcebus murinus (lemur)

rattus norvegiucs

lint checks

explicit gene-id/symbol checks for additional species

slightly generalized test-gene-bump-dry-run

fix set over enum

lint

speed up tests by putting ontology query behind lru cache

support some subspecies

gencode infer species by gene prefix

lint

lint check