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Taxonova

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taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3

4ffc1bd 5 days ago

ssu
Fix the rRNA guard rejecting every short amplicon, and make it fast 2 months ago
static
taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 5 days ago
templates
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
test_fixtures
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
__init__.py

0 Bytes
Upload 142 files about 1 year ago
app.py

28.4 kB
taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 5 days ago
classifier.py

11.5 kB
taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 5 days ago
inputs.py

18.1 kB
Inputs: the alphabet error states what is accepted and does not call a text file protein 9 days ago
jobs.py

4.36 kB
New web app: composition plots, count tables, downloads; taxonova 26.10.1 15 days ago
model_cache.py

4.53 kB
Model cache: state the measured memory per model 10 days ago
model_catalog.py

8.16 kB
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
outputs.py

14.7 kB
Unknown at a rank counts as no name in the reference: apart from the named taxa and from Unclassified in the summary, the confidence caption and the charts (dark grey); downloads unchanged 9 days ago
package_adapter.py

22.7 kB
taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 5 days ago
prefilter_build_check.sh

5.19 kB
Halve the pre-filter's cost by consulting the two SSU models in turn 2 months ago
rrna_prefilter.py

15.5 kB
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
taxonomy_profiles.py

2.22 kB
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
test_api.py

19.5 kB
taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 5 days ago
test_inputs.py

9.87 kB
Inputs: the alphabet error states what is accepted and does not call a text file protein 9 days ago
test_model_cache.py

1.6 kB
Parity tests for every registry model on reads that exercise the species gate and group labels 10 days ago
test_model_catalog.py

2.79 kB
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
test_outputs.py

12.7 kB
Unknown at a rank counts as no name in the reference: apart from the named taxa and from Unclassified in the summary, the confidence caption and the charts (dark grey); downloads unchanged 9 days ago
test_package_adapter.py

15 kB
taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 5 days ago
test_parity.py

15.2 kB
taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 5 days ago
test_prefilter_search_plan.py

4.94 kB
Halve the pre-filter's cost by consulting the two SSU models in turn 2 months ago
test_reference_selector.py

6.34 kB
Region list in region order: V4, V4-V5, V3-V4, V5-V7, full-length 16S, then the rRNA operon 9 days ago
test_rrna_prefilter_gaps.py

2.28 kB
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
test_sequence_ids.py

3.83 kB
Backend for 26.11: classify through the package, operating point by default, lazy models, registry-only catalogue 10 days ago
test_taxonomy_profiles.py

8.8 kB
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture 9 days ago
test_threshold_parity.py

4.24 kB
Backend for 26.11: classify through the package, operating point by default, lazy models, registry-only catalogue 10 days ago