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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)
21 lines
1.4 KiB
Markdown
21 lines
1.4 KiB
Markdown
# Semantic Description of `obiseq` Package Functionalities
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This Go package provides **sequence filtering predicates** for biological sequences, integrated with taxonomic validation and hierarchy analysis.
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- `IsAValidTaxon(taxonomy, ...bool) SequencePredicate`:
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Returns a predicate that checks whether a sequence has an associated valid taxon in the given taxonomy.
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Optionally supports *auto-correction* of outdated/incorrect `taxid` values to match the current taxonomy node.
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- `IsSubCladeOf(taxonomy, parent) SequencePredicate`:
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Filters sequences whose taxonomic assignment is a descendant (sub-clade) of the specified `parent` taxon.
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- `IsSubCladeOfSlot(taxonomy, key) SequencePredicate`:
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Enables filtering based on a *sequence attribute* (e.g., `"taxon"` or `"classification"`) that holds a taxonomic label.
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Validates the label against the taxonomy, then checks if the sequence’s assigned taxon falls under it.
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- `HasRequiredRank(taxonomy, rank) SequencePredicate`:
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Ensures the sequence’s taxon is assigned at or below a specified rank (e.g., `"species"`, `"genus"`).
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Validates the requested `rank` against taxonomy’s rank list; exits on invalid input.
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All predicates follow a functional, composable design pattern (`SequencePredicate = func(*BioSequence) bool`), enabling flexible pipeline construction (e.g., filtering, classification validation).
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