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29 lines
1.5 KiB
Markdown
29 lines
1.5 KiB
Markdown
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# Aho-Corasick-Based Sequence Analysis in `obicorazick`
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This Go package provides efficient pattern-matching utilities for biological sequence data, leveraging the Aho-Corasick algorithm.
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## Core Components
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- **`AhoCorazickWorker(slot string, patterns []string) obiseq.SeqWorker`**
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Builds *multiple* Aho-Corasick matchers in parallel (batched to manage memory), then returns a `SeqWorker` function.
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- Scans each sequence *forward* and its reverse complement.
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- Counts total matches (`slot`), forward-only (`_Fwd`) and reverse-complement-specific (`_Rev`) matches.
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- Attaches match counts as sequence attributes.
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- **`AhoCorazickPredicate(minMatches int, patterns []string) obiseq.SequencePredicate`**
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Compiles a *single* matcher and returns a predicate function.
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- Returns `true` if the number of matches ≥ `minMatches`.
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- Useful for filtering sequences (e.g., taxonomic assignment or contamination detection).
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## Technical Highlights
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- **Batched compilation**: Large pattern sets are split into chunks (default `10⁷` patterns/batch) to avoid memory overload.
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- **Parallelization**: Matcher construction uses goroutines, scaled by `obidefault.ParallelWorkers()`.
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- **Progress tracking**: Optional CLI progress bar via `progressbar/v3`, enabled globally.
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- **Logging & debugging**: Uses Logrus for info/debug messages; logs match counts per sequence.
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## Use Cases
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- Rapid screening of sequences against large reference databases (e.g., primers, barcodes, contaminants).
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- Filtering or annotating sequences based on pattern presence/abundance.
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