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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)
34 lines
2.1 KiB
Markdown
34 lines
2.1 KiB
Markdown
# Sequence Predicate Framework in `obiseq`
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This Go package provides a flexible and composable predicate system for filtering biological sequences (`BioSequence`) based on diverse criteria.
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## Core Concepts
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- **`SequencePredicate`**: A function type `func(*BioSequence) bool`, enabling conditional logic on sequences.
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- **Predicate Composition**: Supports logical operations (`And`, `Or`, `Xor`, `Not`) and chaining.
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- **Paired-end Support**: Predicates can be adapted to consider read pairs via `PredicateOnPaired` and `PairedPredicat`, with modes:
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- `ForwardOnly`: Only the forward read is evaluated.
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- `ReverseOnly`, `And`, `Or`, `AndNot`, `Xor`: Combine forward and reverse evaluations.
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## Built-in Predicates
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| Predicate | Description |
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|-----------|-------------|
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| `HasAttribute(name)` | Checks if a sequence has an annotation with the given name. |
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| `IsAttributeMatch(name, pattern)` | Tests if a named annotation matches the provided regex (case-sensitive). |
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| `IsMoreAbundantOrEqualTo(count)` / `IsLessAbundantOrEqualTo(count)` | Filters by sequence abundance (count field). |
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| `IsLongerOrEqualTo(length)` / `IsShorterOrEqualTo(length)` | Filters by sequence length. |
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| `OccurInAtleast(sample, n)` | Checks if the sequence appears in at least *n* samples (via description stats). |
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| `IsSequenceMatch(pattern)` | Matches the raw sequence against a regex (case-insensitive). |
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| `IsDefinitionMatch(pattern)` | Matches the definition/description line against a regex. |
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| `IsIdMatch(pattern)` / `IsIdIn(ids...)` | Filters by sequence ID using regex or explicit set. |
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| `ExpressionPredicat(expression)` | Evaluates a custom boolean expression (via OBILang) using annotations and sequence metadata. |
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## Design Highlights
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- **Null-safe**: `nil` predicates are handled gracefully in compositions.
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- **Extensible**: Custom predicates can be defined and combined seamlessly.
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- **Logging & Safety**: Invalid regex patterns or expression syntax trigger fatal errors; runtime evaluation issues emit warnings.
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This framework enables powerful, declarative filtering pipelines for high-throughput sequencing data analysis.
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