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ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
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Taxonomy input from taxcheck #173

Closed kpenn88 closed 2 years ago

kpenn88 commented 2 years ago

I am wondering if there are any plans to take the results from TaxCheck and apply them to the Genus species required by the Yaml, this would help automate large scale annotations efforts.

thibaudnis commented 2 years ago

Hello - thank you for the suggestion. We have considered making this an option, but don't have a timeline for implementing it. It is nice to hear that there is support for it!

silvtal commented 2 years ago

Hello - thank you for the suggestion. We have considered making this an option, but don't have a timeline for implementing it. It is nice to hear that there is support for it!

I would be interested as well!

thibaudnis commented 2 years ago

@kpenn88 and @silvtal : we added this feature in 2022-02-10.build5872 . There is a --auto-correct-tax flag in pgap.py to override the organism provided in the input YAML file, if the taxcheck predicts a different organism with high confidence. You will need to use --auto-correct-tax in combination with --taxcheck. Please let us know how that works for you! Thanks