Eric Coissac
6acafa7f2c
Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
36 lines
2.1 KiB
Markdown
36 lines
2.1 KiB
Markdown
# select
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Project and/or aggregate the genome columns of an index into a new (or in-place) index. Where [`filter`](filter.md) selects rows (kmers), `select` operates on columns (genomes): grouping several genomes into one aggregated column, reordering columns, or dropping some.
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```bash
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obikmer select SOURCE (--output OUTPUT | --in-place) [OPTIONS]
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```
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## Arguments
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| Argument | Description |
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|---|---|
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| `SOURCE` | Source index directory |
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## Options
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| Option | Default | Description |
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|---|---|---|
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| `--output` | — | Output index directory (mutually exclusive with `--in-place`) |
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| `--in-place` | off | Rewrite the source index in place (mutually exclusive with `--output`) |
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| `-f, --force` | off | Overwrite an existing output directory |
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| `--group NAME:PRED` | none | Define a named group of genomes by predicate (repeatable; mutually exclusive with `--aggregate-by`) |
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| `--group-op NAME:OP` | none | Aggregation operator for a named group |
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| `--aggregate-by KEY` | none | Automatically create one group per distinct value of a metadata key (mutually exclusive with `--group`) |
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| `--aggregate-op OP` | none | Aggregation operator applied to every auto-generated group |
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| `--select COL,...` | all columns | Output columns, in order (group names or genome labels) |
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| `--presence-threshold` | `0` | Minimum count for a genome to be considered a carrier (logical operators only) |
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## Aggregation operators
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`any`, `all`, `none` (logical, evaluated against `--presence-threshold`), `sum`, `min`, `max` (numeric, count index only). If a group's operator is left unspecified, it defaults to `any` when the source is a presence/absence index and `sum` when it stores counts.
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A `select` never changes the underlying kmer set — only the per-genome data (counts or presence) is rewritten, so an unaggregated pass-through column (a plain genome label in `--select`) is a cheap copy.
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At least one of `--output`/`--in-place` is required, and at least one output column must be defined; every name listed in `--select` must resolve to either a defined group or an existing genome label. See [Genome predicates and taxonomy paths](predicates.md) for the predicate syntax used by `--group`.
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