obitools4/autodoc/docmd/pkg/obiseq/subseq_test.md

obiseq Package: Subsequence Extraction Functionality

The Subsequence() method enables extraction of a contiguous segment from biological sequence data (BioSequence). It supports both linear and circular (wrapped) slicing.

• Input Parameters:

  • from, to: 0-based inclusive indices defining the slice range.
  • circular: boolean flag enabling wrap-around when from > to.

• Behavior:

  • For linear (circular = false), from ≤ to, and indices within bounds [0, len(seq)).
  • For circular (circular = true), allows wrap-around (e.g., from=3, to=2 on a 4-mer yields indices [3,0,1]).
  • Validates inputs: returns descriptive errors for:
    • from > to (non-circular),
    • out-of-bounds indices (< 0 or ≥ length),
    • invalid ranges.

• Quality Support:

  • When sequence includes base quality scores (BioSequenceWithQualities), the method preserves corresponding sub-slice of Quality[].

• Return Value:

  • Returns a new BioSequence (or subclass) instance containing the extracted subsequence and its optional qualities.

• Use Case:

  • Ideal for region-of-interest extraction (e.g., primer binding sites, domain segments), especially in circular genomes or plasmids.

• Testing:

  • Unit tests (TestSubsequence) cover valid/invalid inputs, circular/non-circular modes, and quality consistency.

This functionality provides robust, semantics-aware slicing for biosequence manipulation in Go.