26 lines
849 B
Markdown
26 lines
849 B
Markdown
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# annotate
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Add or update genome metadata of an index from a CSV file, or dump the current metadata as CSV.
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```bash
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obikmer annotate INDEX --csv FILE [OPTIONS]
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obikmer annotate INDEX --dump
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```
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## Arguments
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| Argument | Description |
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|---|---|
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| `INDEX` | Index directory to annotate (modified in place) |
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## Options
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| Option | Default | Description |
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|---|---|---|
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| `--csv` | — | CSV file of metadata to apply (must contain an id column); required unless `--dump` is used |
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| `--sep` | `,` | CSV field separator |
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| `--id-col` | `id` | Name of the column containing genome labels |
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| `--na-value` | `NA` | Value meaning "remove this field" (deletes the existing key if present) |
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| `--no-overwrite` | off | Do not overwrite existing metadata keys |
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| `--dump` | off | Print all genome metadata as CSV to stdout instead of applying a file |
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