Updating version support for starmar, amrfinderplus, kmerresistance - summarize output breaks about hamronization HOT 4 OPEN

Hi, thanks for flagging this, it seems like there is an issue with generating headers.

The intended behaviour is that if multiple reports are passed to hamronize at once that only the first report writes a header. This is to allow a user to pass say 10 reports in and pipe them all to the same output file. Clearly something is going wrong here though.

Just so I fix the right thing, can you clarify exactly how what command you are running for hamronize for one of the outputs missing a head?

from hamronization.

For sure - those without headers have been run with the following command on a folder of multiple reports such as:

hamronize amrfinderplus amr_amrfinder/*.tsv --output hamronize_amrfinder --input_file_name amrfinderplus --analysis_software_version v3.11.14 --reference_database_version 2023-11-15.1

I tried running hamronize on a single report from each tool listed above and the summarize output does look at expected (attached)
results_single.txt

from hamronization.

Weird, I'm struggling to reproduce the behaviour with the AFP outputs I have to hand.

Could you clone the repository and enter it:

git clone https://github.com/pha4ge/hAMRonization; cd hAMRonization

Then run the following command:

hamronize amrfinderplus test/data/dummy/amrfinderplus/report.tsv test/data/raw_outputs/amrfinderplus/report_nucleotide.tsv test/data/raw_outputs/amrfinderplus/report_protein.tsv --output hamronize_test --input_file_name amrfinderplus --analysis_software_version v3.11.14 --reference_database_version 2023-11-15.1

Does hamronize_test have a header?

Also does the same behaviour happen if you use the json output format and summarize those, e.g.:

hamronize amrfinderplus amr_amrfinder/*.tsv --output hamronize_amrfinder.json --input_file_name amrfinderplus --analysis_software_version v3.11.14 --reference_database_version 2023-11-15.1 --format json

hamronize summarize hamronize_amrfinder.json

from hamronization.

Re: hamronize_test - it looks like the header was repeated once for each input, output attached
hamronize_test.txt

Re: json - the json file appears correct as far as I can tell (attached), but the summarize command produces only a header, no data
hamronize_amrfinder.json

Also attached a few of my outputs from amrfinderplus if that's helpful
20231115_sample03_amrfinder.txt
20231128_sample02_amrfinder.txt

from hamronization.