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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)
32 lines
1.6 KiB
Markdown
32 lines
1.6 KiB
Markdown
# Newick Format Export Functionality in `obiformats`
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This Go package provides utilities to export taxonomic data into the **Newick format**, a standard for representing phylogenetic trees.
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## Core Components
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- `Tree`: A struct modeling a node in a Newick tree, containing:
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- `Children`: list of child nodes (nested trees),
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- `TaxNode`: reference to a taxonomic entry (`obitax.TaxNode`),
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- `Length`: optional branch length (evolutionary distance).
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- **`Newick()` methods**:
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- `Tree.Newick(...)`: Recursively generates a Newick string for the subtree.
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Supports optional annotations: `scientific_name`, `taxid` (with `'@'` for rank), and branch lengths.
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- Package-level `Newick(...)`: Converts a full taxon set into a Newick tree string using the root node from `taxa.Sort().Get(0)`.
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- **Writing Functions**:
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- `WriteNewick(...)`: Asynchronously writes the Newick representation to any `io.WriteCloser`.
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- Accepts an iterator over taxa (`*obitax.ITaxon`).
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- Validates single-taxonomy input.
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- Applies compression (via `obiutils.CompressStream`) if configured via options (`WithOption`).
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- `WriteNewickToFile(...)`: Convenience wrapper to write directly to a file.
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- `WriteNewickToStdout(...)`: Outputs Newick tree to standard output.
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## Configuration Options
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Options (e.g., `WithScientificName`, `WithTaxid`, `WithRank`) control annotation content and behavior (e.g., file closing, compression).
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## Semantic Summary
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The module enables **conversion of hierarchical taxonomic datasets into structured Newick trees**, supporting rich node labeling for downstream phylogenetic or bioinformatic tools.
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