problem when running gene_classification.ipynb
hello,geneformer team, I want to reproduce the great work,
but when I run ###gene_classification.ipynb,
cc.prepare_data(input_data_file="path/to/gc-30M_sample50k.dataset",
output_directory=output_dir,
output_prefix=output_prefix)
I encountered the following problem,
TypeError: label_classes() missing 1 required positional argument: 'id_class_dict'
May I ask how to solve it?
Thank you for your reply.
hello,I think I found an inconsistency between the actual parameters and the formal parameters.
In classifier.py, in line 469 there is:
elif self.classifier == "gene":
data, id_class_dict = cu.label_classes(
self.classifier, data, self.gene_class_dict, self.nproc
)
but in classifier_utils.py, in line 97 there is
def label_classes(classifier, data, gene_class_dict, nproc, id_class_dict).
so they are not compatible.
Could you tell me how to solve it correctly?
Thank you for your reply
Thank you for bringing this to our attention - we pushed a fix to address it.