[BUG] Antibiotic column from RGI output not being pulled into "antimicrobial agent" column

[jhawkey]

Describe the bug
I've taken some output from the latest version of RGI (web portal on CARD website) and run it through hamronization. The ouptut table from RGI includes an "Antibiotic" column, as well as a drug class column. However this information is being lost during hamronization, as it isn't being pulled through to hamronization's "antimicrobial agent" column.

Input

hamronize rgi 2025-01-14_110652.908_KPN2009.fasta_RGIOutput.txt --format tsv --output 2025-01-14_110652.908_KPN2009_hamronize.txt --analysis_software_version 6.0.3 --reference_database_version 3.3.0 --input_file_name 2025-01-14_110652.908_KPN2009.fasta_RGIOutput.txt

Input file
2025-01-14_110652.908_KPN2009.fasta_RGIOutput.txt

Output file
2025-01-14_110652.908_KPN2009_hamronize.txt

hAMRonization Version
1.1.8

Expected behavior
Would have expected the Antibiotic column to be pulled into the antimicrobial agent col in the hamronized output.

[zwets]

Hi Jane,

Looks like this field was added to RGI output, as well "hit start" and "hit end". I'll check if there were more additions we could include and submit a patch.

Cheers
Marco

[fmaguire]

That's great @zwets and thanks for letting me know @jhawkey, I think @raphenya had been planning to update the RGI parser but it fell off the radar!