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gagneurlab / MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing
MIT License
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"stop iteration" trouble #53

Open rominageysels opened 3 years ago

rominageysels commented 3 years ago

Hi, I'm trying to run MMSplice using the google colab notebook online. For some reason, I wasn't able to download MMSplice from kipoi directly in my computer... maybe it was because I have Windows, not Linux OS. I got lots of errors I just couldn't deal with. Anyways, I tried to run this model online to assess my VCF and in this part:

predict_save(model, dl, output_csv, pathogenicity=True, splicing_efficiency=True)

I got this error:

StopIteration Traceback (most recent call last)

in () ----> 1 predict_save(model, dl, output_csv, pathogenicity=True, splicing_efficiency=True) 1 frames /usr/local/lib/python3.7/dist-packages/mmsplice/mmsplice.py in predict_save(model, dataloader, output_csv, batch_size, progress, pathogenicity, splicing_efficiency) 272 splicing_efficiency=splicing_efficiency) 273 --> 274 return df_batch_writer(df_iter, output_csv) 275 276 /usr/local/lib/python3.7/dist-packages/mmsplice/utils.py in df_batch_writer(df_iter, output) 41 42 def df_batch_writer(df_iter, output): ---> 43 df = next(df_iter) 44 with open(output, 'w') as f: 45 df.to_csv(f, index=False) StopIteration: Obviously, I can't run the next lines because something is missing there. I think may be this is a bug, but i'm not sure (I'm not an expert in programming) Would you advice me to try installing MMSplice in another computer with LinuxOS instead of running the google colab? I will be very grateful if you can help me solve this issue, and if someone got the same error please let me know too. --Romina--
s6juncheng commented 3 years ago

Could you please double-check whether your VCF file is empty or the format is incorrect?

rominageysels commented 3 years ago

I checked, the VCF file is not empty. I created it using Data Slicer from Ensembl(GRCh37), then downloaded as a compressed file.