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WGLab / PhenoSV

PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
MIT License
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Missing `features_set.csv` file #13

Closed corinsexton closed 1 month ago

corinsexton commented 1 month ago

Hi there,

I just installed PhenoSV and my first run is showing that the features_set.csv file is missing. I used the command to download the full model using setup.sh which completed successfully. It looks like the rest of the files are in the directory. What's the best way for me to download this file?

FileNotFoundError: [Errno 2] No such file or directory: '/phenosv_data/data/features_set.csv'

Here's the contents of the data directory:

data dir

Thank you,

Corinne

Karenxzr commented 1 month ago

Hi Corinne, I see you have features_set_light.csv there but missing features_set.csv. There may be a problem when you trying to run setup.sh. However, I think you can manually make a copy of featuremaster_scu1026.csv (fig1 below), and change the root folder paths to your folder storing all features (fig2 below where my data locates at /Volumes/G-DRIVE USB-C/...). This should be similar with features_set_light.csv

Alternatively, you can rerun the script of python3 $current_dir/phenosv/setup.py --path "$fpath/data" to create features_set.csv for setting up the path.

Please let me know if it works.

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corinsexton commented 1 month ago

Looks like the issue was in the last line of setup.sh.

python3 $current_dir/phenosv/setup.py --path "$fpath/data"

I wasn't in the correct conda environment and this part was dropped. Rerunning that last line fixed it. Thanks!