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feat(initial release): First commit.
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‎.github/workflows/build-publish.yml

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name: Version, build, publish
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on:
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push:
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branches:
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- main
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jobs:
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semantic_release_next_version:
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name: Next version
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-node@v3
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with:
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cache: npm
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node-version: 16
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- run: npm install
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- run: npx semantic-release --dry-run
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id: semantic_release
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- uses: actions/upload-artifact@v3
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with:
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name: semantic-release
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path: |
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gtdb_itol_decorate/__init__.py
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CHANGELOG.md
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retention-days: 1
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outputs:
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version: ${{ steps.semantic_release.outputs.version }}
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build_python:
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name: Python build
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runs-on: ubuntu-latest
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needs: semantic_release_next_version
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if: needs.semantic_release_next_version.outputs.version != ''
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steps:
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- uses: actions/checkout@v3
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- uses: actions/download-artifact@v3
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with:
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name: semantic-release
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- uses: actions/setup-python@v4
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with:
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python-version: '3.8'
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- run: |
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python -m pip install -U setuptools wheel
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python setup.py sdist bdist_wheel
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- uses: actions/upload-artifact@v3
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with:
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name: pypi
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path: dist/*
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retention-days: 1
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test_python_sdist:
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name: Python test *.tar.gz
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runs-on: ubuntu-latest
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needs: build_python
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steps:
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- uses: actions/download-artifact@v3
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with:
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name: pypi
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path: dist
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- uses: actions/setup-python@v4
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with:
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python-version: '3.8'
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- run: python -m pip install dist/*.tar.gz
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test_python_wheel:
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name: Python test *.whl
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runs-on: ubuntu-latest
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needs: build_python
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steps:
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- uses: actions/download-artifact@v3
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with:
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name: pypi
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path: dist
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- uses: actions/setup-python@v4
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with:
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python-version: '3.8'
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- run: python -m pip install dist/*.whl
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semantic_release_publish:
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name: Publish to GitHub
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needs: [test_python_sdist, test_python_wheel]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-node@v3
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with:
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cache: npm
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node-version: 16
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- run: npm install
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- run: npx semantic-release
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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upload_pypi:
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name: Publish to PyPI
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needs: [semantic_release_publish]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/download-artifact@v3
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with:
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name: pypi
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path: dist
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- uses: actions/setup-python@v4
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with:
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python-version: '3.8'
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- run: |
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python -m pip install -U twine
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twine upload dist/*
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}

‎.gitignore

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# Distribution / packaging
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.Python
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build/
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_build/
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_static/
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_templates/
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develop-eggs/
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dist/
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downloads/
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# Pyre type checker
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.pyre/
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# PyCharm
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.idea/
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# OS
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.DS_Store
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*.cpp
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*.c
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docs/build/
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docs/source/generated/
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/target
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wheelhouse/
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# Node modules
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node_modules/
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# RST files
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docs/*.rst
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!docs/index.rst
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‎.releaserc

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{
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"tagFormat": "v${version}",
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"branches": [
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"main"
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],
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"plugins": [
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"@semantic-release/commit-analyzer",
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"@semantic-release/release-notes-generator",
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[
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"@semantic-release/exec",
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{
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"verifyReleaseCmd": "sed -i \"s/.*__version__.*/__version__ = '${nextRelease.version}'/g\" gtdb_itol_decorate/__init__.py && echo ::set-output name=version::${nextRelease.version}"
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}
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],
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[
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"@semantic-release/changelog",
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{
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"changelogFile": "CHANGELOG.md"
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}
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],
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[
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"@semantic-release/git",
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{
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"assets": [
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"CHANGELOG.md",
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"gtdb_itol_decorate/__init__.py"
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],
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"message": "chore(release): ${nextRelease.version} [skip ci]\n\n${nextRelease.notes}"
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}
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],
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[
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"@semantic-release/github"
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]
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]
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}

‎README.md

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# gtdb-itol-decorate
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Creates iTOL files for tree decoration, given a set of GTDB genomes.

‎gtdb_itol_decorate/__init__.py

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__title__ = 'gtdb_itol_decorate'
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__description__ = 'Creates iTOL files for tree decoration, given a set of GTDB genomes.'
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__url__ = 'https://github.com/Ecogenomics/gtdb-itol-decorate'
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__version__ = '1.0.0'
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__author__ = 'Aaron Mussig'
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__author_email__ = 'aaronmussig@gmail.com'
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__license__ = 'GPL-3.0'
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__bug_url__ = 'https://github.com/Ecogenomics/gtdb-itol-decorate'
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__doc_url__ = 'https://github.com/Ecogenomics/gtdb-itol-decorate'
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__src_url__ = 'https://github.com/Ecogenomics/gtdb-itol-decorate'

‎gtdb_itol_decorate/__main__.py

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import os
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from pathlib import Path
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import dendropy
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import typer
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from gtdb_itol_decorate.decorate import decorate_tree
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from gtdb_itol_decorate.gtdb import load_taxonomy_file, get_taxon_to_phylum
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from gtdb_itol_decorate.itol import get_phylum_to_lca, get_phylum_colours, write_color_datastrip, \
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get_internal_nodes_with_labels, write_internal_node_labels, write_tree_colours, write_collapse_file, \
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write_popup_file
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from gtdb_itol_decorate.newick import load_newick_file, load_newick_to_tree, validate_dendropy_namespace, \
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get_canonical_mapping, validate_sets, strip_tree_labels, set_node_desc_taxa, set_taxon_label_for_internal_nodes
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from gtdb_itol_decorate.util import log
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def main(tree_path: Path, tax_path: Path, out_dir: Path):
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log(f'Creating output directory: {out_dir}')
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out_dir.mkdir(exist_ok=True)
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log(f'Reading tree from: {tree_path}')
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tree = load_newick_to_tree(str(tree_path))
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log(f'Found {len(tree.leaf_nodes()):,} leaf nodes in the tree.')
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validate_dendropy_namespace((x.label for x in tree.taxon_namespace))
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d_canonical_to_gid = get_canonical_mapping((x.label for x in tree.taxon_namespace))
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log(f'Reading taxonomy from: {tax_path}')
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d_tax = load_taxonomy_file(str(tax_path), set(d_canonical_to_gid.keys()))
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log(f'Read the taxonomy for {len(d_tax):,} genomes.')
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validate_sets(set(d_canonical_to_gid.keys()), set(d_tax.keys()))
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log('Reverse mapping taxon to phylum')
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d_taxon_to_phylum = get_taxon_to_phylum(d_tax)
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log('Annotating internal nodes with descendant taxa')
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set_node_desc_taxa(tree)
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set_taxon_label_for_internal_nodes(tree, d_tax)
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log('Getting the last common ancestor of each phylum.')
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d_phylum_to_lca = get_phylum_to_lca(tree)
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d_phylum_palette = get_phylum_colours(d_phylum_to_lca)
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write_color_datastrip(d_phylum_to_lca, d_phylum_palette, out_dir / 'itol_dataset_strip_phylum.txt')
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log('Making tree compatible with iTOL (stripping labels)')
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strip_tree_labels(tree)
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path_tree_out = out_dir / f'{tree_path.name}_stripped'
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tree.write_to_path(path_tree_out, schema='newick', suppress_rooting=True, unquoted_underscores=True)
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log('Writing internal node labels')
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d_int_label_to_lca = get_internal_nodes_with_labels(tree)
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write_internal_node_labels(d_int_label_to_lca, out_dir / 'itol_labels.txt')
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log('Getting tree colour palette')
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write_tree_colours(tree, d_taxon_to_phylum, out_dir / 'itol_tree_colours.txt', d_phylum_palette)
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log('Writing popup information file')
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write_popup_file(tree, d_tax, out_dir / 'itol_popup.txt')
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log('Writing collapse files')
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write_collapse_file(d_int_label_to_lca, out_dir / 'itol_collapse_phylum.txt', 'p__')
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write_collapse_file(d_int_label_to_lca, out_dir / 'itol_collapse_class.txt', 'c__')
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write_collapse_file(d_int_label_to_lca, out_dir / 'itol_collapse_order.txt', 'o__')
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write_collapse_file(d_int_label_to_lca, out_dir / 'itol_collapse_family.txt', 'f__')
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write_collapse_file(d_int_label_to_lca, out_dir / 'itol_collapse_genus.txt', 'g__')
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log('Done.')
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if __name__ == "__main__":
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typer.run(main)

‎gtdb_itol_decorate/decorate.py

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from collections import defaultdict
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def decorate_tree(tree, d_gid_to_tax):
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d_node_to_leaf_taxa = defaultdict(set)
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for node in tree.postorder_node_iter():
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# desc_taxa = get_node_desc_taxa(node)
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print(node)
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# Create a mapping from the taxon to each gid
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d_taxon_to_gids = defaultdict(set)
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for gid, taxon in d_gid_to_tax.items():
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d_taxon_to_gids[taxon.p.value].add(gid)
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d_taxon_to_gids[taxon.c.value].add(gid)
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d_taxon_to_gids[taxon.o.value].add(gid)
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d_taxon_to_gids[taxon.f.value].add(gid)
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d_taxon_to_gids[taxon.g.value].add(gid)
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d_taxon_to_gids[taxon.s.value].add(gid)
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# Find the highest node that forms a monophyletic group
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d_node_to_taxa = defaultdict(set)
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for taxon, gids in d_taxon_to_gids.items():
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mrca_node = tree.mrca(taxon_labels=gids)
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# This is the seed node, so we can't decorate it
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if mrca_node.parent_node is None:
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continue
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d_node_to_taxa[mrca_node].add(taxon)
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return d_node_to_taxa

‎gtdb_itol_decorate/gtdb.py

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from collections import defaultdict
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from typing import Dict
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from gtdblib.taxon.rank import TaxonRank
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from gtdblib.taxon.taxon import Taxon
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from gtdblib.taxonomy.taxonomy import Taxonomy
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from gtdb_itol_decorate.util import canonical_gid
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def load_taxonomy_file(path: str, limit_to_gids: set):
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gtdb_ranks = [TaxonRank.DOMAIN, TaxonRank.PHYLUM, TaxonRank.CLASS,
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TaxonRank.ORDER, TaxonRank.FAMILY, TaxonRank.GENUS,
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TaxonRank.SPECIES]
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out = dict()
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with open(path) as f:
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for line in f.readlines():
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gid, tax = line.strip().split('\t')
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gid = canonical_gid(gid)
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if gid not in limit_to_gids:
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continue
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if gid in out:
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raise Exception(f'Duplicate genome id found: {gid}')
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ranks = tax.split(';')
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if len(ranks) != 7:
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raise Exception(f'Invalid taxonomy for {gid} (expected 7 ranks): {tax}')
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d_rank_to_taxon = dict()
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for rank, taxon_rank in zip(ranks, gtdb_ranks):
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taxon = Taxon(taxon_rank, rank)
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d_rank_to_taxon[taxon_rank.value[0]] = taxon
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taxonomy = Taxonomy(**d_rank_to_taxon)
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out[gid] = taxonomy
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return out
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def get_taxon_to_phylum(d_tax: Dict[str, Taxonomy]):
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out = dict()
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for gid, taxonomy in d_tax.items():
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for rank in ('c', 'o', 'f', 'g', 's'):
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taxon = getattr(taxonomy, rank).value
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out[taxon] = taxonomy.p.value
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return out
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