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🍱 Added all ensembl species DBs (#487)
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* 🍱 Added all ensembl species dbs

* πŸ’š Fix
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sunnyosun authored Jul 31, 2023
1 parent 0007d54 commit 982eede
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Showing 2 changed files with 21 additions and 3 deletions.
16 changes: 14 additions & 2 deletions bionty/sources/sources.yaml
Original file line number Diff line number Diff line change
@@ -1,13 +1,25 @@
version: "0.2.2"
version: "0.2.3"
Species:
ensembl:
vertebrate:
vertebrates:
release-110:
url: https://ftp.ensembl.org/pub/release-110/species_EnsemblVertebrates.txt
release-109:
url: https://ftp.ensembl.org/pub/release-109/species_EnsemblVertebrates.txt
release-108:
url: https://ftp.ensembl.org/pub/release-108/species_EnsemblVertebrates.txt
bacteria:
release-57:
url: https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-57/species_EnsemblBacteria.txt
fungi:
release-57:
url: http://ftp.ensemblgenomes.org/pub/fungi/release-57/species_EnsemblFungi.txt
metazoa:
release-57:
url: http://ftp.ensemblgenomes.org/pub/metazoa/release-57/species_EnsemblMetazoa.txt
plants:
release-57:
url: https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-57/species_EnsemblPlants.txt
name: Ensembl
website: https://www.ensembl.org
Gene:
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8 changes: 7 additions & 1 deletion tests/entities/test_species.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import bionty as bt


def test_ensemble_species_inspect_name():
def test_ensembl_species_inspect_name():
df = pd.DataFrame(
index=[
"spiny chromis",
Expand All @@ -21,3 +21,9 @@ def test_ensemble_species_inspect_name():
expected_series = pd.Series([True, True, True, True, False])

assert inspect.equals(expected_series)


def test_ensembl_species_species():
for sp in ["bacteria", "plants", "fungi", "metazoa"]:
df = bt.Species(species=sp).df()
assert df.shape[0] > 10

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