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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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diffsplice_fishers_exact generates bogus error if input file is missing #282

Open diekhans opened 11 months ago

diekhans commented 11 months ago

Copy and paste the exact command you tried to run

../flair/bin/diffsplice_fishers_exact known_diffSplice/flair.diffsplice.ir.events.quant.tsv H0C H0N
known_fisher/out.fishers.H0C.H0N.flair.diffsplice.ir.events.quant.tsv

however, the input file does not exist known_diffSplice/flair.diffsplice.ir.events.quant.tsv

How did you install Flair?

  1. git cloned the current repository

What happened?

usage: diffsplice_fishers_exact events.quant.tsv colname1 colname2 out.fishers.tsv

which seems to indicate a parameter is missing instead of the input file missing

What else do we need to know? This program doesn't use argparse and handles errors in a manner that requires users to read the code to understand what it did wrong.

diekhans commented 11 months ago

this will also happen with diff_iso_usage, maybe others