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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)
30 lines
1.4 KiB
Markdown
30 lines
1.4 KiB
Markdown
# `obiseq` Package: Subsequence Extraction Functionality
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The `Subsequence()` method enables extraction of a contiguous segment from biological sequence data (`BioSequence`). It supports both linear and circular (wrapped) slicing.
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- **Input Parameters**:
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- `from`, `to`: 0-based inclusive indices defining the slice range.
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- `circular`: boolean flag enabling wrap-around when `from > to`.
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- **Behavior**:
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- For linear (`circular = false`), `from ≤ to`, and indices within bounds `[0, len(seq))`.
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- For circular (`circular = true`), allows wrap-around (e.g., `from=3, to=2` on a 4-mer yields indices `[3,0,1]`).
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- Validates inputs: returns descriptive errors for:
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- `from > to` (non-circular),
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- out-of-bounds indices (`< 0` or `≥ length`),
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- invalid ranges.
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- **Quality Support**:
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- When sequence includes base quality scores (`BioSequenceWithQualities`), the method preserves corresponding sub-slice of `Quality[]`.
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- **Return Value**:
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- Returns a new `BioSequence` (or subclass) instance containing the extracted subsequence and its optional qualities.
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- **Use Case**:
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- Ideal for region-of-interest extraction (e.g., primer binding sites, domain segments), especially in circular genomes or plasmids.
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- **Testing**:
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- Unit tests (`TestSubsequence`) cover valid/invalid inputs, circular/non-circular modes, and quality consistency.
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This functionality provides robust, semantics-aware slicing for biosequence manipulation in Go.
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