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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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fix: universe extensions in gapfill.py #146

Closed BenjaSanchez closed 2 years ago

BenjaSanchez commented 2 years ago

Hi! I was trying to use gapfill as a standalone function for a model, but I kept getting OSError: Failed to load universe, in spite of using a standard universe like "grampos". After some digging, I discovered that in commit cd57c56 the carve script was adapted to read the .xml.gz universe files instead of the .xml ones (the latter which were deleted in the same commit); however, gapfill was not adapted in the same way, which makes it unable to find the universe files. This PR fixes that.

cdanielmachado commented 2 years ago

Hi Benjamin, thanks a lot :)