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docs(scripts): organize README
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tamslo committed Oct 10, 2024
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Expand Up @@ -89,6 +89,14 @@ Run `python run_analysis.py <PATH_TO_BACKUP> [--correct]` to analyze annotations
and optionally correct what can be corrected easily in
`<PATH_TO_BACKUP>_corrected_<TIMESTAMP>.base64.json`.

### Drug annotation checks

| Check | Description | `--correct`ed | Only for single-gene results* |
| ----- | ----------- | ------------- | ----------------------------- |
| `brand_whitespace` | Drug brand names should not have leading or trailing white space. |||

### Guideline annotation checks

| Check | Description | `--correct`ed | Only for single-gene results* |
| ----- | ----------- | ------------- | ----------------------------- |
| `has_consult` | Is "consult your pharmacist..." included in recommendation? |||
Expand All @@ -97,7 +105,6 @@ and optionally correct what can be corrected easily in
| `yellow_warning` | Yellow warning level should be present when the red warning level does not apply but the implication contains "may not work" or "side effects" or the recommendation contains non-standard dose. |||
| `green_warning` | Green warning level should be applied in all non-red and non-yellow cases and when the recommendation states "at standard dose" or similar formulations. |||
| `none_warning` | None warning level should be applied in all not handled warning level cases. |||
| `brand_whitespace` | Drug brand names should not have leading or trailing white space. |||
| `metabolization_before_consequence` | Metabolization implications should come before consequences. |||

\* Skips guidelines with multiple genes unless all results but one are missing
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