mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
36 lines
2.1 KiB
Markdown
36 lines
2.1 KiB
Markdown
|
# `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.
|