codecov[bot]
commented
1 year ago Codecov Report
Patch coverage: 31.80% and project coverage change: -0.09 :warning:
Comparison is base (
6637426) 27.59% compared to head (5fe8961) 27.50%.
Additional details and impacted files
```diff @@ Coverage Diff @@ ## dev #321 +/- ## ========================================== - Coverage 27.59% 27.50% -0.09% ========================================== Files 45 50 +5 Lines 5349 5748 +399 ========================================== + Hits 1476 1581 +105 - Misses 3873 4167 +294 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `27.50% <31.80%> (-0.09%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) | Coverage Δ | | |---|---|---| | [autometa/binning/large\_data\_mode.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvYmlubmluZy9sYXJnZV9kYXRhX21vZGUucHk=) | `0.00% <0.00%> (ø)` | | | [autometa/config/databases.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvY29uZmlnL2RhdGFiYXNlcy5weQ==) | `0.00% <0.00%> (ø)` | | | [autometa/config/utilities.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvY29uZmlnL3V0aWxpdGllcy5weQ==) | `25.00% <ø> (ø)` | | | [autometa/validation/benchmark.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdmFsaWRhdGlvbi9iZW5jaG1hcmsucHk=) | `0.00% <0.00%> (ø)` | | | [autometa/validation/cami.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdmFsaWRhdGlvbi9jYW1pLnB5) | `0.00% <0.00%> (ø)` | | | [autometa/taxonomy/majority\_vote.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdGF4b25vbXkvbWFqb3JpdHlfdm90ZS5weQ==) | `13.53% <11.53%> (+0.83%)` | :arrow_up: | | [autometa/binning/summary.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvYmlubmluZy9zdW1tYXJ5LnB5) | `41.48% <18.18%> (-0.38%)` | :arrow_down: | | [autometa/taxonomy/lca.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdGF4b25vbXkvbGNhLnB5) | `9.37% <19.04%> (+0.57%)` | :arrow_up: | | [autometa/taxonomy/gtdb.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdGF4b25vbXkvZ3RkYi5weQ==) | `21.01% <21.01%> (ø)` | | | [autometa/common/utilities.py](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvY29tbW9uL3V0aWxpdGllcy5weQ==) | `23.35% <37.50%> (+0.65%)` | :arrow_up: | | ... and [10 more](https://codecov.io/gh/KwanLab/Autometa/pull/321?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) | | ... and [1 file with indirect coverage changes](https://codecov.io/gh/KwanLab/Autometa/pull/321/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) 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=KwanLab). 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=KwanLab):umbrella: View full report in Codecov by Sentry.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.
updated to propagate contigs without blast hits to unclassified.fna
The code I showed Friday worked. I was keeping the unfiltered contigs due to a mistake in my bash script and it worked correctly after testing. The only part I haven't tested in an autometa run is the list comprehension in line 288 of vote.py but it worked fine in my jupyter notebook when making sure I was getting the right contigs and no extras.
Worth noting that the docstring I added for taxonomydatabase.UNCLASSIFIED is not building, but this may be an upstream issue per #311