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