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How to select mouse database? #250

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zhoutianrui-tongji opened this issue Apr 19, 2021 · 1 comment
Open

How to select mouse database? #250

zhoutianrui-tongji opened this issue Apr 19, 2021 · 1 comment

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@zhoutianrui-tongji
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I do "pyensembl install --release 102 --species mouse" .it works.
but when i do this :

from pyensembl import EnsemblRelease
data = EnsemblRelease(102,specise="mouse")

ValueError: Missing genome data file from ftp://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens/Homo_sapiens.GRCh38.102.gtf.gz. Run pyensembl install --release 102 --species homo_sapiens

@gabnasello
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gabnasello commented Sep 30, 2022

That's a bit late but for those facing the same issue, the species argument of the EnsemblRelease class requires an object of the class pyensembl.species.Species. Thus, just type:

from pyensembl import EnsemblRelease
from pyensembl.species import mouse

# release 107 uses mouse reference genome GRCm39
data = EnsemblRelease(107, species = mouse)

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