mirror of https://github.com/metabarcoding/obitools4.git synced 2026-04-30 12:00:39 +00:00

Files

T

Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

Taxonomic Analysis Functions in `obiseq` Package

This module provides tools for assigning taxonomic labels to biological sequences using a reference taxonomy.

TaxonomicDistribution(taxonomy):
Returns a map from taxonomic nodes to read counts, based on taxid annotations in the sequence metadata. It validates taxids against the taxonomy and enforces strict handling of aliases.
LCA(taxonomy, threshold):
Computes the Lowest Common Ancestor (LCA) of all taxonomic assignments for a sequence, weighted by their abundances.
- Iteratively traverses upward from each taxon’s path in the taxonomy tree.
- At each level, computes the relative weight (rmax) of the most frequent taxon.
- Stops when rmax < threshold, returning:
  • the LCA taxon,
  • its confidence score (rans), and
  • total read count used.
AddLCAWorker(...):
Creates a SeqWorker function to annotate sequences with LCA results:
- Sets attributes like <slot>_taxid, <slot>_name, and <slot>_error (rounded to 3 decimals).
- Automatically appends _taxid if missing in slot_name.

All functions integrate with the OBITools4 ecosystem, supporting robust taxonomic inference for metabarcoding workflows.

Taxonomic Analysis Functions in obiseq Package