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Kuanhao-Chao / LiftOn

🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies
http://ccb.jhu.edu/lifton
GNU General Public License v3.0
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What does '-E'/evaluation mode do? #4

Closed Andy-B-123 closed 1 month ago

Andy-B-123 commented 2 months ago

Hi, thank you for this tool and for your thorough and helpful documentation and examples!

I'm looking through the options and see the '-E' flag labelled as 'Run LiftOn in evaluation mode'.

When I try and run this with the examples (eg the HoneyBee one) it produces an error? eg:

lifton -g HAv3.1_genomic.gff -o lifton.gff3 -copies ASM1932182v1_genomic.fna HAv3.1_genomic.fna -E

proceeds to start running normally and then errors at:

>> Creating target database :  lifton.gff3
gffutils database build failed with lifton.gff3 cannot be found and does not appear to be a URL

Is 'Evaluation mode' more of a testing feature? Thanks!

Kuanhao-Chao commented 1 month ago

Hi @Andy-B-123,

Yes, the '-E' flag for 'Evaluation mode' in LiftOn is designed primarily for internal testing and debugging purposes.

Please simply remove the -E argument, and it should work correctly. Please let me know if you encounter any problems. Thanks for your feedback! We will update the documentation.