[BUG] Redundant results not merging

[marchoeppner]

Describe the bug
Maybe not a bug, but at least some confusion as to what hamronize can and cannot merge. I have generated amr calls with abricate using 5 different databases bundled with abricate (card, argannot, etc) and was expected hamronize to be able to merge these into a non-redundant set. This is not the case, it seems - possibly because some databases use the same gene symbol, but slightly different gene names. Is this expected?

AMEA2707761.ecoli_vf.txt:SAMEA2707761.fasta contig00012 135971 138775 + eae 1-2805/2805 =============== 0/0 100.00 100.00 ecoli_vf
gi:15804220 intimin adherence protein
SAMEA2707761.vfdb.txt:SAMEA2707761.fasta contig00012 135971 138375 + eae 1-2401/2820 ========/====.. 9/20 84.86 91.38 vfdb A

These two entries are both for eae and will end up as separate entries in the final summary..

Input
hamronize abricate *.txt --format json --analysis_software_version 1.0.1 --reference_database_version 2021-Mar-27 --output test.json
hamronize summarize test.json -t tsv -o out.tsv

Input file

abricate.zip

Error log

hAMRonization Version
1.1.4 (cannot see any abricate related changes in subsequent releases)

Expected behavior
I would expect different abricate database results to be merged into a non-redundant set

Screenshots

Desktop (please complete the following information):

• OS: AlmaLinux 9.4
• Browser ...
• Version [e.g. 22]

Additional context
Add any other context about the problem here.
If applicable, include dependency versions such as pandas version and Python version.