obitools4/autodoc/docmd/pkg/obiiter/fragment.md

IFragments Functionality Overview

The IFragments() function in the obiiter package implements a parallelized sequence fragmentation pipeline for biological sequences. It is designed to split long nucleotide or protein sequences into smaller, overlapping fragments while preserving metadata and enabling concurrent processing.

Core Parameters

• minsize: Minimum sequence length to skip fragmentation.
• length: Desired fragment size (in bases/amino acids).
• overlap: Number of overlapping residues between consecutive fragments.
• size, nworkers: Batch size and number of worker goroutines (currently unused in active logic).

Workflow

1. Batch Sorting: Input sequences are batched and sorted for efficient processing.
2. Parallel Fragmentation:
   • Each worker processes a subset of batches independently using goroutines.
   • For each sequence longer than minsize, it is split into overlapping fragments of length length with step size = length - overlap.
   • The final fragment is extended to cover the remainder (fusion mode), avoiding tiny trailing pieces.
3. Resource Management:
   • Original sequences are recycled (s.Recycle()) to optimize memory usage.
   • Fragments are reassembled into batches, sorted by source and order, then rebatched to respect memory/size limits.

Key Features

• Overlap handling: Ensures contiguous coverage without gaps.
• Memory efficiency: Uses recycling and batched output.
• Scalability: Leverages Go concurrency via nworkers.
• Error safety: Panics on subsequence errors (e.g., invalid indices).

Use Case

Ideal for preparing long-read sequencing data (e.g., PacBio, Nanopore) or assembled contigs for downstream analysis requiring fixed-length inputs (e.g., k-mer indexing, ML inference).