Parses taxonomic information from tip labels using the specified format and returns a data.frame of group assignments. Intended for use as a stable library API by external workflows (e.g., Snakemake/Nextflow).
Usage
parse_taxonomy(
labels,
rank,
format = "auto",
custom_patterns = NULL,
taxonomy_levels = NULL,
delimiter_mode = "reverse"
)Arguments
- labels
Character vector of tip labels
- rank
Taxonomic rank (abbreviation or full name)
- format
Format: "auto", "embedded", "GTDB", "Silva", "NCBI", "custom_rank", "custom_regex"
- custom_patterns
Custom regex patterns (required when format = "custom_regex")
- taxonomy_levels
Custom taxonomy level configuration (list with codes and names)
- delimiter_mode
Character. Embedded parsing strategy: "reverse", "greedy", "segment".