obitools4/autodoc/docmd/pkg/obilua/obiseqslice.md

obilua Package: Lua Bindings for BioSequence Slicing

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.

Core Features

• Type Registration: Registers BioSequenceSlice as a userdata type in Lua with metatable support.
• Constructor: new([capacity]) creates a new slice (optionally pre-sized).
• Indexing & Assignment: slice[i] = seq or seq = slice[i], with bounds checking.
• Dynamic Operations:
  • push(seq): Append a sequence.
  • pop(): Remove and return the last sequence.
• Length Query: len() returns number of sequences in slice.

Output Formatting

Provides multiple export methods to format all contained sequences:

• fasta([format]): Returns FASTA string (supports "json" or "obi" headers).
• fastq([format]): Returns FASTQ string (same format options as above).
• string([format]): Smart formatter:
  • Uses FASTQ if all sequences have quality scores.
  • Falls back to FASTA otherwise.

Design Notes

• All methods validate input types and indices.
• Format selection is optional; defaults to "obi" header style unless specified as "json".
• Integrates with obiseq.BioSequence and formatting utilities from the OBItools4 ecosystem.

This enables Lua users to process NGS data (e.g., FASTA/FASTQ) interactively within pipelines, leveraging Go’s performance and Lua’s expressiveness.