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usage predicates
Eric Coissac edited this page 2026-09-12 14:00:23 +02:00
Table of Contents

Genome predicates and taxonomy paths

Several commands (filter, select, dump, unitig) select or group genomes using the same predicate language over genome metadata (see annotate for attaching metadata to a genome).

Predicate syntax

Form Meaning
* or all Matches every genome (case-insensitive)
key=v1|v2 Genome's key metadata equals one of the listed values
key!=v Genome's key metadata does not equal v
key~path Genome's key metadata (a taxonomy path) matches path (ancestry match)
key!~path Genome's key metadata does not match path

A genome whose metadata does not contain key at all cannot be classified by that predicate and is excluded from the relevant group's quorum count.

Multiple --ingroup predicates are combined with AND; multiple --outgroup predicates are combined with OR. When both an ingroup and an outgroup predicate would match the same genome, ingroup classification wins.

Taxonomy paths

A metadata value is treated as a taxonomy path when it starts with the literal prefix taxonomy:/; any other value is treated as a plain string and only supports =/!=.

taxonomy:/segment1@rank1/segment2@rank2/...

Each segment is a name, optionally annotated with a rank (e.g. @family, @genus, @species); ranks are optional and can be mixed within a path. The @ character is reserved inside taxonomy paths and cannot appear in segment names or rank labels.

Path matching (~ / !~)

Matching compares segment names only (ranks are informational, not part of the match), with anchoring controlled by leading/trailing /:

Pattern Matches
A/B anywhere in the path
/A/B at the start of the path (prefix)
A/B$ at the end of the path (suffix)
/A/B$ the entire path (exact)

A rank-qualified query, key@rank=value, matches only when the path's segment at that specific rank equals value.

Example

obikmer filter source -o output --ingroup "taxon~/Betulaceae/Betula"

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