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wilkelab / Opfi

A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
https://opfi.readthedocs.io/
MIT License
21 stars 5 forks source link

e_value was being passed as a float to `subprocess.run` but it needs … #74

Closed jimrybarski closed 4 years ago

jimrybarski commented 4 years ago

…to be a string. Resolves #72

jimrybarski commented 4 years ago

This might only happen when you pass evalue in as a float to begin with in Pipeline.add_seed_step(). Not sure why we never saw this before because I was using an old script to test this and I don't see anything in the commit history that would explain why this is failing now.

alexismhill3 commented 4 years ago

I recently modified these methods so that they use subprocess.run to execute the command instead of biopython's NCBI blast wrappers. I think subprocess expects the command to be a list of strings so this error makes sense - not sure why my integration tests didn't also break though

alexismhill3 commented 4 years ago

Also did not mean to close this lol