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

[ilypopv]

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!

[ilypopv]

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!

[gaworj]

Hi, thank you for updating the tool. I have installed the newest version and when tried my kraken2 data generated on EuPathDB:

krakenparser -i . -o krakenparser_fungi_out -fungi
KrakenParser by Ilia V. Popov
╭───────────────────────────────────────────────────────────────────── Traceback (most recent call last) ─────────────────────────────────────────────────────────────────────╮
│ /home/jang/miniconda3/envs/krakenparser/lib/python3.14/site-packages/krakenparser/krakenparser.py:151 in main_callback │
│ │
│ 148 │ │ logging.basicConfig(level=logging.INFO, handlers=[log_handler]) │
│ 149 │ │ │
│ 150 │ │ try: │
│ ❱ 151 │ │ │ run_pipeline( │
│ 152 │ │ │ │ input_dir=input_dir, │
│ 153 │ │ │ │ output_dir=output_dir, │
│ 154 │ │ │ │ keep_human=keep_human, │
│ │
│ /home/jang/miniconda3/envs/krakenparser/lib/python3.14/site-packages/krakenparser/pipeline.py:147 in run_pipeline │
│ │
│ 144 │ │ │ _log.info("Skipping: %s", f.name) │
│ 145 │ │ │ continue │
│ 146 │ │ out_name: str = f.stem + ".MPA.TXT" │
│ ❱ 147 │ │ kreport_to_mpa(f, mpa_dir / out_name, display_header=True) │
│ 148 │ │
│ 149 │ mpa_files: list[Path] = sorted(mpa_dir.glob("*.MPA.TXT")) │
│ 150 │ if not mpa_files: │
│ │
│ /home/jang/miniconda3/envs/krakenparser/lib/python3.14/site-packages/krakenparser/mpa/transform2mpa.py:132 in kreport_to_mpa │
│ │
│ 129 │ │ │ if report_vals is None: │
│ 130 │ │ │ │ continue │
│ 131 │ │ │ │
│ ❱ 132 │ │ │ name, level_num, level_type, all_reads, percents = report_vals │
│ 133 │ │ │ │
│ 134 │ │ │ # Safely drop unclassified sequencing categories ('U') │
│ 135 │ │ │ if level_type == "U": │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
ValueError: not enough values to unpack (expected 5, got 0)

Here is my example kraken2 report file:

head -n 20 F1-report.txt
98.65 30180356 30180356 U 0 unclassified
1.35 414081 0 R 1 root
1.35 414081 1 R1 131567 cellular organisms
1.35 414079 987 D 2759 Eukaryota
1.35 411641 0 D1 33154 Opisthokonta
1.35 411641 234 K 4751 Fungi
1.33 407156 293 K1 451864 Dikarya
1.32 404569 78 P 4890 Ascomycota
1.32 404482 137 P1 716545 saccharomyceta
1.32 403009 0 P2 147538 Pezizomycotina
1.32 403009 1816 P3 716546 leotiomyceta
1.30 396879 290 C 147545 Eurotiomycetes
1.30 396531 642 C1 451871 Eurotiomycetidae
1.29 395411 409 O 5042 Eurotiales
1.29 394791 1301 F 1131492 Aspergillaceae
1.14 349124 14950 G 5052 Aspergillus
0.68 209439 6503 G1 2720872 Aspergillus subgen. Fumigati
0.66 202168 184526 S 746128 Aspergillus fumigatus
0.04 11055 11055 S1 451804 Aspergillus fumigatus A1163
0.02 6587 6587 S1 330879 Aspergillus fumigatus Af293

Any hints?

Bests,
Jan