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.
1305 lines
22 KiB
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1305 lines
22 KiB
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<h1 id="genome-predicates-and-taxonomy-paths">Genome predicates and taxonomy paths</h1>
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<p>Several commands (<a href="../filter/"><code>filter</code></a>, <a href="../select/"><code>select</code></a>, <a href="../dump/"><code>dump</code></a>, <a href="../unitig/"><code>unitig</code></a>) select or group genomes using the same predicate language over genome metadata (see <a href="../annotate/"><code>annotate</code></a> for attaching metadata to a genome).</p>
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<h2 id="predicate-syntax">Predicate syntax</h2>
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<table>
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<thead>
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<tr>
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<th>Form</th>
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<th>Meaning</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>*</code> or <code>all</code></td>
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<td>Matches every genome (case-insensitive)</td>
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</tr>
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<tr>
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<td><code>key=v1\|v2</code></td>
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<td>Genome's <code>key</code> metadata equals one of the listed values</td>
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</tr>
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<tr>
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<td><code>key!=v</code></td>
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<td>Genome's <code>key</code> metadata does not equal <code>v</code></td>
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</tr>
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<tr>
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<td><code>key~path</code></td>
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<td>Genome's <code>key</code> metadata (a taxonomy path) matches <code>path</code> (ancestry match)</td>
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</tr>
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<tr>
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<td><code>key!~path</code></td>
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<td>Genome's <code>key</code> metadata does not match <code>path</code></td>
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</tr>
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</tbody>
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</table>
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<p>A genome whose metadata does not contain <code>key</code> at all cannot be classified by that predicate and is excluded from the relevant group's quorum count.</p>
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<p>Multiple <code>--ingroup</code> predicates are combined with AND; multiple <code>--outgroup</code> predicates are combined with OR. When both an ingroup and an outgroup predicate would match the same genome, ingroup classification wins.</p>
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<h2 id="taxonomy-paths">Taxonomy paths</h2>
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<p>A metadata value is treated as a taxonomy path when it starts with the literal prefix <code>taxonomy:/</code>; any other value is treated as a plain string and only supports <code>=</code>/<code>!=</code>.</p>
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<div class="highlight"><pre><span></span><code>taxonomy:/segment1@rank1/segment2@rank2/...
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</code></pre></div>
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<p>Each segment is a name, optionally annotated with a rank (e.g. <code>@family</code>, <code>@genus</code>, <code>@species</code>); ranks are optional and can be mixed within a path. The <code>@</code> character is reserved inside taxonomy paths and cannot appear in segment names or rank labels.</p>
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<h3 id="path-matching">Path matching (<code>~</code> / <code>!~</code>)</h3>
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<p>Matching compares segment names only (ranks are informational, not part of the match), with anchoring controlled by leading/trailing <code>/</code>:</p>
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<table>
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<thead>
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<tr>
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<th>Pattern</th>
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<th>Matches</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>A/B</code></td>
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<td>anywhere in the path</td>
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</tr>
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<tr>
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<td><code>/A/B</code></td>
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<td>at the start of the path (prefix)</td>
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</tr>
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<tr>
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<td><code>A/B$</code></td>
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<td>at the end of the path (suffix)</td>
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</tr>
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<tr>
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<td><code>/A/B$</code></td>
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<td>the entire path (exact)</td>
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</tr>
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</tbody>
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</table>
|
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<p>A rank-qualified query, <code>key@rank=value</code>, matches only when the path's segment at that specific rank equals <code>value</code>.</p>
|
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<h3 id="example">Example</h3>
|
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<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span><span class="nb">source</span><span class="w"> </span>-o<span class="w"> </span>output<span class="w"> </span>--ingroup<span class="w"> </span><span class="s2">"taxon~/Betulaceae/Betula"</span>
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</code></pre></div>
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