method files missing

[LinFe11]

I’m trying to run rnaincoder.py in RNAonly mode, but the pipeline fails when processing RNA feature methods. For example, running:

python rnaincoder.py
-t RNAonly
-a /home/user/rna_sequences.fasta
-l /home/user/rna_labels.csv
-o ./out
-d 1
-s csvnpy
-n 4
-c 8
-m svm

KeyError: 'K-mer (1D)'

I checked dictMeMatch in Dict_methods.py. Some keys like 'K-mer (1D)' are missing by default, and even after manually adding them, the program still fails. It seems several RNA feature methods may not be properly registered or loaded in the current version.

Could you provide guidance on how to correctly configure RNAonly mode so that all standard RNA features are recognized and processed?

Thanks for your help!

[Yunxia-wang]

Thank you for the message. I find the previous link for method file is not effective. So I have upload the necessary files to the method folder. Please run it according to the command. Let me know if you have any questions.

[LinFe11]

Thanks for your reply. Unfortunately there are still files missing. I keep running into this error: ModuleNotFoundError: No module named 'methods._04_kmer_counts_molmap'

Could you check on your side if you can run the code?

Best