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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)
14 lines
1.2 KiB
Markdown
14 lines
1.2 KiB
Markdown
# `obiseq.Subsequence` Functionality Overview
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The `Subsequence()` method extracts a contiguous segment from a biological sequence (`BioSequence`), supporting both linear and circular topologies.
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- **Input validation**: Checks ensure `from < to` (unless circular), positions are non-negative, and bounds respect sequence length.
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- **Circular handling**: Positions exceeding the sequence length wrap around using modular arithmetic; debug logs record corrections.
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- **Linear extraction**: When `from < to`, it slices the underlying nucleotide/peptide sequence and, if present, its quality scores.
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- **Circular extraction**: When `from > to`, it concatenates two linear segments: from `from` → end, and start → `to`.
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- **Metadata preservation**: Quality scores (if available) and annotations are copied to the new subsequence.
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- **ID formatting**: The resulting sequence ID is suffixed with `[from..to]` (1-based indexing).
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- **Mutation tracking**: A private `_subseqMutation()` adjusts stored pairing mismatch positions by subtracting the extraction shift, ensuring coordinate consistency post-extraction.
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This enables robust subsequence generation for genomic analysis workflows involving circular genomes (e.g., plasmids) or fragmented reads.
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