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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
42 lines
2.3 KiB
Markdown
42 lines
2.3 KiB
Markdown
# Semantic Description of `obiseq` Language Extensions
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The `package obiseq` extends the [Gval](https://github.com/PaesslerAG/gval) expression language with domain-specific functions tailored for bioinformatics and data processing. It integrates utility helpers from `obiutils` to provide type-flexible, robust operations over sequences and collections.
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## Core Functionalities
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- **Data Inspection**:
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`len`, `ismap`, `isvector` — retrieve size and type information.
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- **Aggregation & Comparison**:
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`min`, `max` — compute extremal values in slices/maps (via `obiutils.Min/Max`).
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*(Note: commented-out helper functions suggest prior attempts at manual implementations.)*
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- **Type Conversion**:
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`int`, `numeric` (→ float64), `bool`, `string` — safely coerce arbitrary inputs to target types; fail with fatal logs on invalid data.
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- **String Manipulation**:
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`sprintf`, `subspc` (replace spaces with underscores), `replace` (regex-based substitution), and `substr` — support formatting, normalization, and slicing.
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- **Sequence Analysis (Bioinformatics)**:
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`gc`, `gcskew`, and `composition` — compute nucleotide composition metrics for DNA/RNA sequences (`BioSequence`).
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- `gc`: GC content ratio (excluding ambiguous bases `'o'`)
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- `gcskew`: `(G−C)/(G+C)` asymmetry measure
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- `composition`: returns a map of base counts (e.g., `"a":20.0`, `"g":15.0`)
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- **Element Access**:
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`elementof(seq, idx)` — retrieves item at index/key for slices (`[]interface{}`), maps (`map[string]interface{}`), or strings (by byte position).
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- **Control Flow**:
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`ifelse(cond, then_val, else_val)` — conditional branching within expressions.
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- **Quality Support**:
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`qualities(seq)` — extracts per-base quality scores as a float slice from sequencing reads.
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## Design Principles
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- **Dynamic Typing**: Accepts `...interface{}` arguments for flexibility.
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- **Error Handling**: Uses fatal logging (`log.Fatalf`) on conversion failures; returns typed errors for runtime issues.
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- **Extensibility**: Built atop `gval.Language`, enabling custom expression evaluation in pipelines (e.g., filtering reads via GC thresholds).
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This package serves as a bridge between high-level scripting and low-level biosequence computation, ideal for rule-based filtering or annotation in NGS workflows.
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