extracting specific kingdom

[gaworj]

Hi,

Thanks for providing such a great tool!

I am looking for a way to extract data by specific Kingdom (e.g. Bacteria, Fungi). My goal is to generate separate datasets for each. Is this currently doable within the tool, or is there a recommended workflow for this?

Best regards,
Jan

[iliapopov17]

Hi Jan,

Thanks for the kind words! That's a great feature suggestion.
I’ll most likely implement a dedicated filtering mode for specific kingdoms (like Bacteria and Fungi) in the next update.
In the meantime, here is what you can do:

1. Current Workaround for Viruses

Right now, there is a built-in --deconstruct_viruses flag that allows you to inspect the Viruses domain separately:

KrakenParser --deconstruct_viruses -i data/intermediate/COMBINED.txt -o data/counts_viruses
# Having troubles? Run KrakenParser --deconstruct_viruses -h

I am planning to expand this logic to support Bacteria and Fungi modes soon.

2. Manual Workflow for Bacteria and Fungi

For now, the best workaround is to look at the "Using Individual Modules (Advanced)" section in the README:

1. Generate the combined MPA file using the pipeline.
2. Open the file in any text editor or use command-line tools (like grep or awk) to filter out or delete the rows/kingdoms you don't need.
3. Continue your analysis with the filtered dataset.

Stay tuned for the next release, and thanks again for the feedback!

[iliapopov17]

Hi Jan,
Great news! Version 1.1.0 has just been released! It introduces the exact functionality you were looking for.
You can now extract data by specific kingdoms or domains using dedicated pipeline flags directly from the command line:
• --bacteria
• --fungi
• --viruses
• --archaea
You can also mix and match these options with other flags (for instance, combining --fungi and --keep-human works perfectly).
Please note that the CLI syntax has evolved slightly in recent updates to accommodate these changes. I highly recommend checking out the updated README for a quick refresher on the new structure.
Give it a spin and let me know if it works for your workflow! Once you've had a chance to test it, feel free to drop a comment here so I can close this issue.
Hope the tool serves your research well!