mirror of https://github.com/metabarcoding/obitools4.git synced 2026-04-30 12:00:39 +00:00

Files

T

Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

Aho-Corasick-Based Sequence Analysis in `obicorazick`

This Go package provides efficient pattern-matching utilities for biological sequence data, leveraging the Aho-Corasick algorithm.

Core Components

AhoCorazickWorker(slot string, patterns []string) obiseq.SeqWorker
Builds multiple Aho-Corasick matchers in parallel (batched to manage memory), then returns a SeqWorker function.
- Scans each sequence forward and its reverse complement.
- Counts total matches (slot), forward-only (_Fwd) and reverse-complement-specific (_Rev) matches.
- Attaches match counts as sequence attributes.
AhoCorazickPredicate(minMatches int, patterns []string) obiseq.SequencePredicate
Compiles a single matcher and returns a predicate function.
- Returns true if the number of matches ≥ minMatches.
- Useful for filtering sequences (e.g., taxonomic assignment or contamination detection).

Batched compilation: Large pattern sets are split into chunks (default 10⁷ patterns/batch) to avoid memory overload.
Parallelization: Matcher construction uses goroutines, scaled by obidefault.ParallelWorkers().
Progress tracking: Optional CLI progress bar via progressbar/v3, enabled globally.
Logging & debugging: Uses Logrus for info/debug messages; logs match counts per sequence.

Rapid screening of sequences against large reference databases (e.g., primers, barcodes, contaminants).
Filtering or annotating sequences based on pattern presence/abundance.