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taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation
https://taxpasta.readthedocs.io/
Apache License 2.0
34 stars 7 forks source link

Fix metaphlan tax ID being -1 and combine all unclassified counts #85

Closed Midnighter closed 1 year ago

Midnighter commented 1 year ago
codecov-commenter commented 1 year ago

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (46bf412) 82.03% compared to head (c700feb) 82.03%.

:exclamation: Current head c700feb differs from pull request most recent head 5ddee66. Consider uploading reports for the commit 5ddee66 to get more accurate results

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #85 +/- ## ======================================= Coverage 82.03% 82.03% ======================================= Files 103 103 Lines 1575 1575 Branches 278 278 ======================================= Hits 1292 1292 Misses 242 242 Partials 41 41 ``` | [Impacted Files](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [src/taxpasta/application/service/profile\_reader.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2FwcGxpY2F0aW9uL3NlcnZpY2UvcHJvZmlsZV9yZWFkZXIucHk=) | `86.66% <100.00%> (ø)` | | | [src/taxpasta/domain/model/standard\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2RvbWFpbi9tb2RlbC9zdGFuZGFyZF9wcm9maWxlLnB5) | `100.00% <100.00%> (ø)` | | | [...rc/taxpasta/domain/model/tidy\_observation\_table.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2RvbWFpbi9tb2RlbC90aWR5X29ic2VydmF0aW9uX3RhYmxlLnB5) | `100.00% <100.00%> (ø)` | | | [...rc/taxpasta/domain/model/wide\_observation\_table.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2RvbWFpbi9tb2RlbC93aWRlX29ic2VydmF0aW9uX3RhYmxlLnB5) | `100.00% <100.00%> (ø)` | | | [...rastructure/application/bracken/bracken\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2JyYWNrZW4vYnJhY2tlbl9wcm9maWxlLnB5) | `100.00% <100.00%> (ø)` | | | [...cture/application/centrifuge/centrifuge\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2NlbnRyaWZ1Z2UvY2VudHJpZnVnZV9wcm9maWxlLnB5) | `100.00% <100.00%> (ø)` | | | [...rastructure/application/diamond/diamond\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2RpYW1vbmQvZGlhbW9uZF9wcm9maWxlLnB5) | `100.00% <100.00%> (ø)` | | | [.../infrastructure/application/kaiju/kaiju\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2thaWp1L2thaWp1X3Byb2ZpbGUucHk=) | `100.00% <100.00%> (ø)` | | | [...rastructure/application/kraken2/kraken2\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2tyYWtlbjIva3Jha2VuMl9wcm9maWxlLnB5) | `100.00% <100.00%> (ø)` | | | [...cture/application/krakenuniq/krakenuniq\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2tyYWtlbnVuaXEva3Jha2VudW5pcV9wcm9maWxlLnB5) | `100.00% <100.00%> (ø)` | | | ... and [5 more](https://codecov.io/gh/taxprofiler/taxpasta/pull/85?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None)

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