TALON
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Issue with talon filter
Hi,
I have been trying to run talon filter on my database:
talon_filter_transcripts --db talon/database.db -a Hg38 --maxFracA 0.5 --minCount 1 --minDatasets 3 --o talon/talon_run.csv
And I'm getting an import error:
Traceback (most recent call last):
File "/users/k19022845/.local/bin/talon_filter_transcripts", line 5, in <module>
from talon.post.filter_talon_transcripts import main
File "/users/k19022845/.local/lib/python3.8/site-packages/talon/post/filter_talon_transcripts.py", line 13, in <module>
from . import ab_utils as autils
File "/users/k19022845/.local/lib/python3.8/site-packages/talon/post/ab_utils.py", line 6, in <module>
import scanpy
File "/users/k19022845/.local/lib/python3.8/site-packages/scanpy/__init__.py", line 17, in <module>
from . import datasets, logging, queries, external, get, metrics, experimental
File "/users/k19022845/.local/lib/python3.8/site-packages/scanpy/external/__init__.py", line 4, in <module>
from . import exporting
File "/users/k19022845/.local/lib/python3.8/site-packages/scanpy/external/exporting.py", line 14, in <module>
from pandas.api.types import is_categorical
ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/users/k19022845/.local/lib/python3.8/site-packages/pandas/api/types/__init__.py)
I previously had issues with numpy
, so I installed it to be version 1.22.4
.