Eric Coissac
caf59b5658
Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
1279 lines
22 KiB
HTML
1279 lines
22 KiB
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obikmer — User Guide
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select
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Theory
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Theory
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Kmers and super-kmers
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DNA encoding
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Low-complexity kmer filter
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</a>
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Minimizer selection
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Partitioning and indexing architecture
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Usage
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<span class="md-nav__icon md-icon"></span>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
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Usage
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superkmer
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index
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merge
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filter
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select
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select
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</a>
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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Table of contents
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Arguments
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Options
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Aggregation operators
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query
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dump
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annotate
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<h1 id="select">select</h1>
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<p>Project and/or aggregate the genome columns of an index into a new (or in-place) index. Where <a href="../filter/"><code>filter</code></a> selects rows (kmers), <code>select</code> operates on columns (genomes): grouping several genomes into one aggregated column, reordering columns, or dropping some.</p>
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<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span><span class="k">select</span><span class="w"> </span>SOURCE<span class="w"> </span><span class="o">(</span>--output<span class="w"> </span>OUTPUT<span class="w"> </span><span class="p">|</span><span class="w"> </span>--in-place<span class="o">)</span><span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
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</code></pre></div>
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<h2 id="arguments">Arguments</h2>
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<table>
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<thead>
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<tr>
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<th>Argument</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><code>SOURCE</code></td>
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<td>Source index directory</td>
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</tr>
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</tbody>
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</table>
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<h2 id="options">Options</h2>
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<table>
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<thead>
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<tr>
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<th>Option</th>
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<th>Default</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><code>--output</code></td>
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<td>—</td>
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<td>Output index directory (mutually exclusive with <code>--in-place</code>)</td>
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</tr>
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<tr>
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<td><code>--in-place</code></td>
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<td>off</td>
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<td>Rewrite the source index in place (mutually exclusive with <code>--output</code>)</td>
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</tr>
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<tr>
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<td><code>-f, --force</code></td>
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<td>off</td>
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<td>Overwrite an existing output directory</td>
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</tr>
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<tr>
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<td><code>--group NAME:PRED</code></td>
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<td>none</td>
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<td>Define a named group of genomes by predicate (repeatable; mutually exclusive with <code>--aggregate-by</code>)</td>
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</tr>
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<tr>
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<td><code>--group-op NAME:OP</code></td>
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<td>none</td>
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<td>Aggregation operator for a named group</td>
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</tr>
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<tr>
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<td><code>--aggregate-by KEY</code></td>
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<td>none</td>
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<td>Automatically create one group per distinct value of a metadata key (mutually exclusive with <code>--group</code>)</td>
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</tr>
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<tr>
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<td><code>--aggregate-op OP</code></td>
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<td>none</td>
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<td>Aggregation operator applied to every auto-generated group</td>
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</tr>
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<tr>
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<td><code>--select COL,...</code></td>
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<td>all columns</td>
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<td>Output columns, in order (group names or genome labels)</td>
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</tr>
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<tr>
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<td><code>--presence-threshold</code></td>
|
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<td><code>0</code></td>
|
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<td>Minimum count for a genome to be considered a carrier (logical operators only)</td>
|
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</tr>
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</tbody>
|
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</table>
|
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<h2 id="aggregation-operators">Aggregation operators</h2>
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<p><code>any</code>, <code>all</code>, <code>none</code> (logical, evaluated against <code>--presence-threshold</code>), <code>sum</code>, <code>min</code>, <code>max</code> (numeric, count index only). If a group's operator is left unspecified, it defaults to <code>any</code> when the source is a presence/absence index and <code>sum</code> when it stores counts.</p>
|
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<p>A <code>select</code> 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 <code>--select</code>) is a cheap copy.</p>
|
|
<p>At least one of <code>--output</code>/<code>--in-place</code> is required, and at least one output column must be defined; every name listed in <code>--select</code> must resolve to either a defined group or an existing genome label. See <a href="../predicates/">Genome predicates and taxonomy paths</a> for the predicate syntax used by <code>--group</code>.</p>
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