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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)
32 lines
1.5 KiB
Markdown
32 lines
1.5 KiB
Markdown
# `obilua` Package: Lua Bindings for BioSequence Slicing
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This Go module provides **Lua scripting support** for biological sequence manipulation via the `obilua` package. It exposes a custom Lua type, `"BioSequenceSlice"`, wrapping Go’s `*obiseq.BioSequenceSlice` to enable high-level sequence operations in Lua.
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## Core Features
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- **Type Registration**: Registers `BioSequenceSlice` as a userdata type in Lua with metatable support.
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- **Constructor**: `new([capacity])` creates a new slice (optionally pre-sized).
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- **Indexing & Assignment**: `slice[i] = seq` or `seq = slice[i]`, with bounds checking.
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- **Dynamic Operations**:
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- `push(seq)`: Append a sequence.
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- `pop()`: Remove and return the last sequence.
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- **Length Query**: `len()` returns number of sequences in slice.
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## Output Formatting
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Provides multiple export methods to format all contained sequences:
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- `fasta([format])`: Returns FASTA string (supports `"json"` or `"obi"` headers).
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- `fastq([format])`: Returns FASTQ string (same format options as above).
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- `string([format])`: Smart formatter:
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- Uses FASTQ if *all* sequences have quality scores.
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- Falls back to FASTA otherwise.
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## Design Notes
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- All methods validate input types and indices.
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- Format selection is optional; defaults to `"obi"` header style unless specified as `"json"`.
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- Integrates with `obiseq.BioSequence` and formatting utilities from the OBItools4 ecosystem.
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This enables Lua users to process NGS data (e.g., FASTA/FASTQ) interactively within pipelines, leveraging Go’s performance and Lua’s expressiveness.
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