ystrauch / ci-spliceai__annotation Goto Github PK

Dear Dr Yaron and Developers

Thank you for developing CI-SpliceAI. I think it is a useful improvement to SpliceAI.

I ran into the following error from running CI-SpliceAI. May I seek your assistance?

mamba create -n cis_use python=3.8 tensorflow-gpu cudnn keras -c conda-forge -y
mamba activate cis_use
pip install "cispliceai"
cis-vcf -h

Output:
Traceback (most recent call last):
File "/home/weiyuan/mambaforge/envs/cis_use/bin/cis-vcf", line 5, in
from cispliceai.console import vcf
File "/home/weiyuan/mambaforge/envs/cis_use/lib/python3.8/site-packages/cispliceai/init.py", line 2, in
from .annotation import Annotator, JSONFormatException, AnnotationJob, AnnotationJobWithResults, Annotation, AnnotationCache
File "/home/weiyuan/mambaforge/envs/cis_use/lib/python3.8/site-packages/cispliceai/annotation.py", line 8, in
from cispliceai import const, progress, data
File "/home/weiyuan/mambaforge/envs/cis_use/lib/python3.8/site-packages/cispliceai/data.py", line 65, in
class AnnotatedArea():
File "/home/weiyuan/mambaforge/envs/cis_use/lib/python3.8/site-packages/cispliceai/data.py", line 75, in AnnotatedArea
acceptors: List[int],
NameError: name 'List' is not defined

Notes:
The installation process went fine. I tried version control of dependencies with
mamba create -n cis_use python=3.8 tensorflow-gpu=2.2.0 cudnn=7.6.5.32=hc0a50b0_1 keras=2.4.3 -c conda-forge
but I encountered this error:
Encountered problems while solving:

• nothing provides requested tensorflow-gpu 2.2.0**

Thank you for your attention.

Best Regards
WY

Hi, thank you for your work. I am trying to reproduce the CI-SpliceAI model but running "python create_data.py" results in an assertion error after 93% progress at line 87 "assert len(x) == len(y)".