orthoxml-tools 0.4.1__tar.gz

orthoxml_tools-0.4.1/.github/workflows/publish.yml

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+# publish.yml
+
+name: "Publish"
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  publish:
+    if: startsWith(github.event.head_commit.message, 'release:')
+    name: "Build and Publish"
+    runs-on: ubuntu-latest
+    permissions:
+        contents: write
+        id-token: write
+    
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+    
+      - name: Build
+        run: uv build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://upload.pypi.org/legacy/
+

orthoxml_tools-0.4.1/.github/workflows/test.yml

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+name: "Test"
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+
+jobs:
+  test:
+    name: "Test on Python Versions"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          pip install .
+          pip install '.[test]'
+
+      - name: Run tests
+        run: pytest -vv

orthoxml_tools-0.4.1/.gitignore

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+# Customs
+
+tests_output/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# PyPI configuration file
+.pypirc

orthoxml_tools-0.4.1/.python-version

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+3.13

orthoxml_tools-0.4.1/LEGACY-README.md

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+The `orthoxml-tools` package used to provides a object oriented interface for working with OrthoXML files. This API is deprecated and will be removed in v1.0.0. Please use the new streaming CLI method. the rationale behind this migration mainly comes from memory usage consideration.
+
+# Legacy API Usage
+
+```python
+>>> from orthoxml import OrthoXMLTree
+>>> otree = OrthoXMLTree.from_file("data/sample.orthoxml", validate=True)
+>>> otree
+2025-02-11 11:43:17 - loaders - INFO - OrthoXML file is valid for version 0.5
+OrthoXMLTree(genes=[5 genes], species=[3 species], groups=[0 groups], taxonomy=[0 taxons], orthoxml_version=0.5)
+```
+
+### Filter Based on CompletenessScore at Loading
+```python
+>>> from orthoxml import OrthoXMLTree
+>>> otree = OrthoXMLTree.from_file("data/sample.orthoxml", CompletenessScore_threshold=0.95, validate=True)
+>>> otree
+2025-02-11 11:43:17 - loaders - INFO - OrthoXML file is valid for version 0.5
+OrthoXMLTree(genes=[5 genes], species=[3 species], groups=[0 groups], taxonomy=[0 taxons], orthoxml_version=0.5)
+```
+
+### Accessing Specific Data
+
+*   **Groups**
+
+```python
+>>> otree.groups
+OrthologGroup(taxonId=5, geneRefs=['5'], orthologGroups=[OrthologGroup(taxonId=4, geneRefs=['4'], orthologGroups=[], paralogGroups=[ParalogGroup(taxonId=None, geneRefs=['1', '2', '3'], orthologGroups=[], paralogGroups=[])])], paralogGroups=[])
+```
+
+*   **Genes**
+
+```python
+>>> otree.genes
+defaultdict(orthoxml.models.Gene,
+            {'1': Gene(id=1, geneId=hsa1, protId=None),
+             '2': Gene(id=2, geneId=hsa2, protId=None),
+             '3': Gene(id=3, geneId=hsa3, protId=None),
+             '4': Gene(id=4, geneId=ptr1, protId=None),
+             '5': Gene(id=5, geneId=mmu1, protId=None)})
+```
+
+*   **Taxonomy**
+
+```python
+>>> otree.taxonomy
+Taxon(id=5, name=Root, children=[Taxon(id=3, name=Mus musculus, children=[]), Taxon(id=4, name=Primates, children=[Taxon(id=1, name=Homo sapiens, children=[]), Taxon(id=2, name=Pan troglodytes, children=[])])])
+```
+
+For a more human-readable tree structure:
+
+```python
+>>> print(otree.taxonomy.to_str())
+Root
+├── Mus musculus
+└── Primates
+    ├── Homo sapiens
+    └── Pan troglodytes
+```
+
+*   **Species**
+
+```python
+>>> otree.species
+[Species(name=Homo sapiens, NCBITaxId=9606, genes=[Gene(id=1, geneId=hsa1), Gene(id=2, geneId=hsa2), Gene(id=3, geneId=hsa3)]),
+ Species(name=Pan troglodytes, NCBITaxId=9598, genes=[Gene(id=4, geneId=ptr1)]),
+ Species(name=Mus musculus, NCBITaxId=10090, genes=[Gene(id=5, geneId=mmu1)])]
+```
+
+### Statistics of the OrthoXML tree
+
+*   **Basic Stats**
+```python
+>>> otree.base_stats()
+{'genes': 10,
+ 'species': 3,
+ 'groups': 3,
+ 'taxonomy': 0,
+ 'orthoxml_version': '0.5'}
+```
+
+*   **Gene Number per Taxonomic Level Stats**
+```python
+>>> otree.gene_stats()
+{'5': 4, '3': 3, '4': 3, '2': 6, '1': 10}
+>>> otree.gene_stats(filepath="out.csv", sep=",") # to also writes the stats to file with two columns: taxonId and gene_count
+{'5': 4, '3': 3, '4': 3, '2': 6, '1': 10}
+```
+
+### Manipulate the Tree
+
+* **Split an instance of OrthoXML Tree to separate OrthoXML Trees based on rootHOGs**
+```python
+>>> otrees = otree.split_by_rootHOGs()
+>>> otrees[0].groups
+OrthologGroup(taxonId=1, geneRefs=['1000000002'], orthologGroups=[OrthologGroup(taxonId=2, geneRefs=['1001000001', '1002000001'], orthologGroups=[], paralogGroups=[])], paralogGroups=[])
+```
+
+### Export Options
+
+*   **Orthologous Pairs**
+
+```python
+>>> otree.to_ortho_pairs()
+[('1', '2'), ('1', '3')]
+>>> otree.to_ortho_pairs(filepath="out.csv") # to also writes the pairs to file
+[('1', '2'), ('1', '3')]
+```
+
+*   **Get Orthologous Pairs of an Specific Gene**
+
+```python
+>>> otree.to_ortho_pairs_of_gene("1001000001")
+[('1001000001', '1002000001'), ('1000000002', '1001000001')]
+>>> otree.to_ortho_pairs_of_gene("1001000001", filepath="out.csv") # to also writes the pairs to file
+[('1001000001', '1002000001'), ('1000000002', '1001000001')]
+```
+
+*   **Orthologous Groups**
+
+```python
+>>> otree.to_ogs()
+[['1000000002', '1001000001', '1002000001'],
+ ['1000000003', '1001000002', '1002000002'],
+ ['1000000004', '1001000003', '1002000003']]
+>>> otree.to_ogs(filepath="out.csv") # to also writes the groups to file
+[['1000000002', '1001000001', '1002000001'],
+ ['1000000003', '1001000002', '1002000002'],
+ ['1000000004', '1001000003', '1002000003']]
+```
+
+### Export Options
+
+* **Export Back Manipulated Tree to OrthoXML**
+
+```python
+>>> otree.to_orthoxml()
+<?xml version='1.0' encoding='utf-8'?>
+<orthoXML xmlns="http://orthoXML.org/2011/" version="0.5" origin="orthoXML.org" originVersion="1.0">
+  <species name="Homo sapiens" NCBITaxId="9606">
+...
+  </groups>
+</orthoXML>
+```