obitools4/autodoc/docmd/pkg/obiiter/extract_taxonomy.md

ExtractTaxonomy Function — Semantic Description

The ExtractTaxonomy method is a core utility in the obiiter package, designed to aggregate taxonomic information across biological sequences processed by an iterator.

• Input:

  • A pointer to IBioSequence, representing a sequence iterator over biological data.
  • A boolean flag seqAsTaxa: if true, each full sequence is treated as a single taxonomic unit; otherwise, individual elements within slices are processed separately.

• Process:

  • Iterates through all sequences via iterator.Next() and retrieves each current slice using Get().Slice().
  • For every slice, it calls the underlying .ExtractTaxonomy() method (from obitax), progressively building or updating a shared *obitax.Taxonomy object.
  • Stops and returns immediately upon encountering the first error during taxonomy extraction.

• Output:

  • Returns a fully populated *obitax.Taxonomy object (or partial result if early failure occurs).
  • Returns nil error on success; otherwise, returns the first encountered error.

• Semantic Role:
  Enables scalable taxonomic profiling of high-throughput sequencing data by delegating per-slice extraction logic to the obitax module, while ensuring robust iteration and error handling.

• Dependencies:
  Relies on obitax.Taxonomy for structured taxonomic representation and assumes slices implement the .ExtractTaxonomy() interface.

This function exemplifies a map-reduce-style pattern: mapping taxonomy extraction over slices, and reducing results into a unified taxonomic summary.