NEW: filter_kraken2_classifications action #226
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Codecov ReportAll modified and coverable lines are covered by tests ✅
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## main #226 +/- ##
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+ Coverage 95.60% 95.62% +0.01%
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Files 34 34
Lines 1956 2010 +54
Branches 226 235 +9
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+ Hits 1870 1922 +52
- Misses 48 49 +1
- Partials 38 39 +1 ☔ View full report in Codecov by Sentry. |
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- q2_moshpit/kraken2/tests/data/abundance-filter/outputs-only-unclassified/sample1.output.txt: Language not supported
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- q2_moshpit/kraken2/tests/data/abundance-filter/outputs/sample1.output.txt: Language not supported
- q2_moshpit/kraken2/tests/data/abundance-filter/outputs/sample2.output.txt: Language not supported
- q2_moshpit/kraken2/tests/data/abundance-filter/reports-only-unclassified/sample1.report.txt: Language not supported
- q2_moshpit/kraken2/tests/data/abundance-filter/reports-only-unclassified/sample2.report.txt: Language not supported
- q2_moshpit/kraken2/tests/data/abundance-filter/reports-w-unclassified/sample1.report.txt: Language not supported
- q2_moshpit/kraken2/tests/data/abundance-filter/reports-w-unclassified/sample2.report.txt: Language not supported
- q2_moshpit/kraken2/tests/data/abundance-filter/reports/sample1.report.txt: Language not supported
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Comments suppressed due to low confidence (1)
q2_moshpit/kraken2/classification.py:278
- [nitpick] Consider including the sample_id in the error message for better debugging.
raise ValueError("All Taxonomic bins were filtered by the"
| report_df = report.view(pd.DataFrame) | ||
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|
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| if (len(report_df) == 1): | ||
| raise ValueError("Kraken2 abundance filtering can not be preformed" |
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The word 'preformed' should be 'performed'.
Suggested change
| raise ValueError("Kraken2 abundance filtering can not be preformed" | |
| raise ValueError("Kraken2 abundance filtering can not be performed" |
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misialq
requested changes
Jan 14, 2025
| parameter_descriptions={}, | ||
| output_descriptions={}, | ||
| name='Filter Kraken2 Classifications by Abundance', | ||
| description='...', |
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Should we just put here the text from the "name" field or did you want to keep the ...?
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| input_descriptions={}, | ||
| parameter_descriptions={}, | ||
| output_descriptions={}, |
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Please provide these missing descriptions 🙏
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Hi Bok Lab!
I recently was taking to a collaborator who's area of expertise is metagenomic contaminations/spurious hits. They suggested that I should be preforming low abundance filtering on my data to filter out spurious hits. They suggested that the kraken reports is the best place to filter, so that bracken isn't estimating taxons that were spuriously assigned.
@colinvwood and I develped a methods to allow for filtering the kraken reports by abundance! This method also filters the output files so that the reports and outputs are not out of sync.
Just as a side note: I used this code on a dataset of mine and found that filtering at 0.0001 (which means the taxon has to have roughly 15-60 hits or it gets discarded) retains my diversity signal but minizes the low abundance feature overlap that was happening in my samples!
Let me know if y'all have any questions!