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murphycj / AGFusion

Python package to annotate and visualize gene fusions.
https://www.agfusion.app
MIT License
59 stars 25 forks source link

Unsupported species for H.sapiens ensembl 92 #25

Closed zlskidmore closed 5 years ago

zlskidmore commented 5 years ago

Hi, I'm getting an unsupported species error. Looking at the docs and code this appears to be referencing the pyensembl database correct? I'm using the latest release 1.2 with ensembl version 92. Any suggestions would be appreciated!

Zach

Error

Traceback (most recent call last):
  File "/usr/local/bin/agfusion", line 5, in <module>
    cli.main()
  File "/usr/local/lib/python3.6/dist-packages/agfusion/cli.py", line 535, in main
    assert species in AVAILABLE_ENSEMBL_SPECIES, 'unsupported species!'
AssertionError: unsupported species!

Command

agfusion batch -f star-fusion.fusion_predictions.tsv -a starfusion -db /opt/pyensembl/pyensembl/GRCh38/ensembl92/Homo_sapiens.GRCh38.92.gtf.db -o agfusion
murphycj commented 5 years ago

Zach, the -db flag is for the agfusion prebuilt database, which you can download with “agfusion download” command. Enter “agfusion download -h” for more information.

Let me know if that helps!

zlskidmore commented 5 years ago

yes that was it, thanks for the help! Looks like release 1.2 might not support ensembl 92 as well but rolling that back to 87 worked

murphycj commented 5 years ago

great that you got it working. Actually, there is a more recent version of agfusion available on python pip (v1.24). You can run “pip install agfusion --upgrade”. I haven’t made the release on GitHub yet. It supports Ensembl 92. You can also try that if you want.