FoxoTech / methylcheck

Python-based Illumina methylation array quality control software.
MIT License
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Reinstall new version of methylcheck, file not found error #61

Open viabard opened 2 years ago

viabard commented 2 years ago

When using methylcheck.run_qc() without running any updated methylprep functions, the manifest name is different, so there is a file not found error.


FileNotFoundError                         Traceback (most recent call last)
<ipython-input-6-e73e0aa9d459> in <module>
----> 1 methylcheck.run_qc(initial_folder)

~/opt/anaconda3/lib/python3.8/site-packages/methylcheck/qc_plot.py in run_qc(path)
     54     qc_signal_intensity(meth=meth_df, unmeth=unmeth_df, poobah=poobah)
     55     plot_controls(controls, 'all')
---> 56     plot_beta_by_type(beta_df, 'all')
     57 
     58 

~/opt/anaconda3/lib/python3.8/site-packages/methylcheck/qc_plot.py in plot_beta_by_type(beta_df, probe_type, return_fig, silent, on_lambda)
    550         LOGGER.setLevel(logging.INFO)
    551     else:
--> 552         raise FileNotFoundError("manifest file not found.")
    553 
    554     # merge reference col, filter probes, them remove ref col(s)

FileNotFoundError: manifest file not found.
---------------------------------------------------------------------------
viabard commented 2 years ago

This was fixed by running methylprep.Manifest('epic')