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

obiseq Package: Semantic Overview

The obiseq package provides a robust, thread-safe implementation of biological sequence objects in Go. It defines the core BioSequence type and associated utilities for handling nucleotide sequences (DNA/RNA), quality scores, annotations, features, memory management, and metadata operations.

Core Functionalities

• Construction & Initialization

  • NewEmptyBioSequence(cap) creates an empty sequence with optional preallocated capacity.
  • NewBioSequence(id, seq, def) builds a basic sequence with ID (case-normalized), byte-level sequence ([]byte), and definition.
  • NewBioSequenceWithQualities(...) extends the above with per-base quality scores ([]byte or Quality).

• Accessors & Properties

  • Id(), Definition() return metadata fields.
  • Sequence() returns the normalized (lowercase) sequence as a copy of internal bytes.
  • Len() returns the length (number of bases).
  • String() provides a human-readable sequence string.

• Quality & Feature Support

  • HasQualities() checks if quality scores are present.
  • Qualities(), SetQualities(...) manage per-base quality data (with fallback to default values).
  • Features() retrieves optional feature annotations as a string.

• Annotation System

  • Annotations(), HasAnnotation() allow inspection of arbitrary metadata (key-value map).
  • Thread-safe via internal sync.Mutex, exposed through AnnotationsLock().

• Utility & Safety

  • Recycle() safely resets internal slices and annotations (enables object pooling). Handles nil receivers gracefully.
  • Copy() performs deep copy of all fields, including annotations and locks (new mutex).
  • MD5() computes the MD5 hash of the sequence bytes.

• Analysis Methods

  • Composition() returns a nucleotide count map (a, c, g, t, and 'o' for others), case-insensitive.

All operations are designed with performance, safety (nil-safety, copy semantics), and extensibility in mind—ideal for bioinformatics pipelines requiring immutable or pooled sequence handling.