Feature Array has size of 0?

WGLab / PhenoSV

PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.

MIT License

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Feature Array has size of 0? #8

Closed mjang2000 closed 5 months ago

mjang2000 commented 7 months ago

Hello, I'm running the program for the first time in Python and there is a ValueError for the basic running of the algorithm becaus of a size 0 feature array.

Can you help identify what went wrong?

Karenxzr commented 7 months ago

Hi, it seems the error lies in configuring file location. Can you double confirm the 'config_path' is the right place for storing all the files?

mjang2000 commented 7 months ago

Config has all the correct pathways for all the file names. I manually edited the config because the initiation function didn't work with my file tree

Although "../phenosv_files/data/chromhmm_15.bb" does not exist. How can I change this to "/home/amyjang/phenosv_files/data/chromhmm_15.bb"?

Karenxzr commented 7 months ago

Try running scripts in 'phenosv/setup.py', which basically change the file paths in the csv files of feature_files and scaler_file.

mjang2000 commented 7 months ago

@Karenxzr that worked thanks!

I'm trying to replicate this in the terminal, and I get the following error?

The notebook cell worked fine, and the csv file is formatted correctly based on the sample datasets provided.

mjang2000 commented 7 months ago

Hi team, bumping this in case it was missed.

Karenxzr commented 7 months ago

Can you try to score the given sampledata.csv? It works well on my end.

Karenxzr commented 7 months ago

@mjang2000 The error might be caused by SVs on chromosomes as mentioned in #9 . I fixed the bug, please pull and try it again.