Dear,
I wanted to perform annotations locally or with our cluster. So I made a new conda environment and went with the script available (for colab session) at your website
upon running any cell where I have to import 'annotations', it throws an error as below.
from annotation import get_pretrained_model_genes, check_genes_is_subset
pretrained_scanvi_path = os.path.join(tissue, tissue + "_scanvi_model")
pretrained_scvi_path = os.path.join(tissue, tissue + "_scvi_model")
training_mode='online'
is_subset = False
if training_mode == 'online':
pretrained_genes = get_pretrained_model_genes(pretrained_scvi_path)
query_genes = query_adata.var_names.to_numpy().astype("str")
is_subset = check_genes_is_subset(pretrained_genes, query_genes)
if is_subset and training_mode=='online':
ref_adata = ref_adata[:, pretrained_genes]
else:
training_mode = 'offline'
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
Input In [11], in <cell line: 16>()
1 # !conda install -c conda-forge sortedcontainers --yes
2 # !conda uninstall tensorflow --yes
3 # !conda uninstall tensorboard --yes
(...)
14 # !conda install tensorboard --yes
15 #!conda install -c conda-forge tensorflow --yes
---> 16 from annotation import get_pretrained_model_genes, check_genes_is_subset
17 pretrained_scanvi_path = os.path.join(tissue, tissue + "_scanvi_model")
18 pretrained_scvi_path = os.path.join(tissue, tissue + "_scvi_model")
File /mnt/DATA1/Fibrosis/Fibrosis_2022/Annotation/scripts/annotation.py:14, in <module>
11 import scvi
12 import seaborn as sns
---> 14 from OnClass.OnClassModel import OnClassModel
16 from sklearn import svm
17 from sklearn.ensemble import RandomForestClassifier
File ~/anaconda3/envs/tsapiens/lib/python3.9/site-packages/OnClass/OnClassModel.py:6, in <module>
3 import sys
4 from sklearn.preprocessing import normalize
----> 6 from OnClass.OnClass_utils import *
7 from OnClass.BilinearNN import BilinearNN
9 class OnClassModel:
File ~/anaconda3/envs/tsapiens/lib/python3.9/site-packages/OnClass/OnClass_utils.py:19, in <module>
17 from sklearn.metrics.pairwise import cosine_similarity
18 #from libs import *
---> 19 from sklearn.utils.graph_shortest_path import graph_shortest_path
20 from scipy.sparse.linalg import svds, eigs
22 def get_ontology_parents(GO_net, g, dfs_depth):
ModuleNotFoundError: No module named 'sklearn.utils.graph_shortest_path'
It will be nice if a yaml file for the conda environment or list of versions of each package is provided.
Thanks again and Kind regards,
Saeed
Dear,
I wanted to perform annotations locally or with our cluster. So I made a new conda environment and went with the script available (for colab session) at your website
upon running any cell where I have to import 'annotations', it throws an error as below.
It will be nice if a yaml file for the conda environment or list of versions of each package is provided.
Thanks again and Kind regards,
Saeed