genomic_position_from_gtf
Hafsa-Faeth opened this issue · comments
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I was using genomic_position_from_gtf on my ann dataframe before running infercnv. It has always worked well for me previously but now I keep getting this error:
Any suggestions? Thanks a lot!
Version information
anndata 0.8.0
celltypist 1.3.0
infercnvpy 0.4.0
matplotlib 3.5.1
numpy 1.21.6
pandas 1.5.2
pkg_resources NA
scanpy 1.9.1
scvi 0.19.0
session_info 1.0.0
PIL 9.1.0
absl NA
asttokens NA
attr 21.4.0
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
botocore 1.24.21
brotli NA
certifi 2021.10.08
cffi 1.15.0
charset_normalizer 2.0.12
chex 0.1.5
cloudpickle 2.0.0
contextlib2 NA
cycler 0.10.0
cython_runtime NA
cytoolz 0.11.2
dask 2022.04.1
dateutil 2.8.2
debugpy 1.6.0
decorator 5.1.1
defusedxml 0.7.1
deprecate 0.3.2
docrep 0.3.2
entrypoints 0.4
etils 0.9.0
executing 0.8.3
flax 0.6.3
fsspec 2022.3.0
google NA
graphviz 0.20
gtfparse NA
h5py 3.7.0
hypergeom_ufunc NA
idna 3.3
igraph 0.10.3
ipykernel 6.13.0
ipython_genutils 0.2.0
ipywidgets 7.7.0
jax 0.4.1
jaxlib 0.4.1
jedi 0.18.1
jinja2 3.1.2
joblib 1.1.0
kiwisolver 1.4.2
leidenalg 0.9.1
llvmlite 0.38.0
lz4 4.0.0
markupsafe 2.1.1
matplotlib_inline NA
ml_collections NA
mpl_toolkits NA
msgpack 1.0.3
mudata 0.2.1
multipledispatch 0.6.0
natsort 8.1.0
nbinom_ufunc NA
numba 0.55.1
numpyro 0.10.1
nvidia NA
opt_einsum v3.3.0
optax 0.1.4
packaging 21.3
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
polars 0.15.10
prompt_toolkit 3.0.29
psutil 5.9.0
ptyprocess 0.7.0
pure_eval 0.2.2
pyarrow 6.0.1
pycparser 2.21
pydev_ipython NA
pydevconsole NA
pydevd 2.8.0
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.12.0
pynndescent 0.5.8
pyparsing 3.0.9
pyreadr 0.4.7
pyro 1.8.3
pytorch_lightning 1.7.7
pytz 2022.1
requests 2.27.1
rich NA
ruamel NA
scipy 1.8.0
six 1.16.0
sklearn 1.0.2
snowflake NA
socks 1.7.1
stack_data 0.2.0
statsmodels 0.13.5
tblib 1.7.0
tensorboard 2.11.0
texttable 1.6.7
threadpoolctl 3.1.0
tlz 0.11.2
toolz 0.11.2
torch 1.13.1+cu117
torchmetrics 0.11.0
tornado 6.1
tqdm 4.64.1
traitlets 5.2.1.post0
tree 0.1.8
typing_extensions NA
umap 0.5.3
unicodedata2 NA
urllib3 1.26.9
wcwidth 0.2.5
wrapt 1.14.1
yaml 6.0
zmq 22.3.0
zoneinfo NA
IPython 8.3.0
jupyter_client 7.3.1
jupyter_core 4.10.0
notebook 6.4.11
Python 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:25:59) [GCC 10.3.0]
Linux-5.4.190-107.353.amzn2.x86_64-x86_64-with-glibc2.31
Session information updated at 2023-01-02 14:37
Hi @Hafsa-Faeth,
thanks for reporting this!
Apparently gtfparse returns a polars dataframe instead of a pandas dataframe in the latest version.
This is easy to fix by adding
read_gtf(..., result_type='pandas')For now, you can try to downgrade gtfparse:
pip install "gtfparse<2"Should be fixed in the latest v0.4.1