phenocor 0.2.0__tar.gz

phenocor-0.2.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Monarch Initiative and contributors
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

phenocor-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: phenocor
+Version: 0.2.0
+Summary: A Python package for correlation analysis of HPO annotations in GA4GH phenopacket cohorts
+Author-email: Jing Chen <jing.chen@bih-charite.de>
+Maintainer-email: Peter Robinson <peter.robinson@bih-charite.de>, Daniel Danis <daniel.danis@bih-charite.de>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, Monarch Initiative and contributors
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: homepage, https://github.com/P2GX/phenocor
+Project-URL: repository, https://github.com/P2GX/phenocor.git
+Project-URL: documentation, https://P2GX.github.io/phenocor/
+Project-URL: bugtracker, https://github.com/P2GX/phenocor/issues
+Keywords: Global Alliance for Genomics and Health,GA4GH Phenopacket Schema,Human Phenotype Ontology,GA4GH,HPO
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: hpo-toolkit<0.6,>=0.5.0
+Requires-Dist: phenopackets<3.0,>=2.0.2
+Requires-Dist: scikit-learn<2.0,>=1.6.1
+Requires-Dist: numpy<3.0,>=1.26.4
+Requires-Dist: pandas<3.0,>=2.2.3
+Requires-Dist: plotly>=6.1.1
+Requires-Dist: kaleido>=1.0.0
+Requires-Dist: scipy<2.0,>=1.15.1
+Requires-Dist: joblib<2.0,>=1.4.2
+Requires-Dist: tqdm<5.0,>=4.67.1
+Requires-Dist: statsmodels<1.0,>=0.14.4
+Provides-Extra: test
+Requires-Dist: pytest<8.0.0,>=7.0.0; extra == "test"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material[imaging]<10,>=9.5.10; extra == "docs"
+Requires-Dist: mkdocs-material-extensions<2.0,>=1.3; extra == "docs"
+Requires-Dist: mkdocstrings[python]<1.0,>=0.22; extra == "docs"
+Requires-Dist: mkdocs-gen-files>=0.5.0; extra == "docs"
+Requires-Dist: pillow; extra == "docs"
+Requires-Dist: cairosvg; extra == "docs"
+Dynamic: license-file
+
+# phenocor
+
+**phenocor** is a Python library for analyzing pairwise relationships between Human Phenotype Ontology (HPO) features in [GA4GH Phenopacket](https://www.ga4gh.org/product/phenopackets/) cohorts.
+
+It provides **Pairwise association analysis**, which measures associations between binary phenotype annotations using the phi coefficient and Fisher's exact test.
+
+
+---
+
+## Installation
+
+```bash
+pip install phenocor
+```
+
+
+## Features
+
+* Construction of phenotype matrices from GA4GH Phenopackets, with separate representation of observed, excluded, and unreported HPO annotations
+* Ontology-aware propagation of phenotype annotations
+* Pairwise phenotype association analysis using the phi coefficient, Fisher's exact test, and Benjamini–Hochberg correction, with exclusion of ancestor–descendant HPO term pairs
+* Tabular results and interactive heatmaps, including contingency counts, effective sample sizes, adjusted p-values, and publication provenance where available
+
+
+## Quickstart
+
+```python
+from pathlib import Path
+from google.protobuf.json_format import Parse
+from phenopackets import Phenopacket
+from phenocor import (
+    PhenotypeDatasetBuilder,
+    HPOCorrelationAnalyzer,
+)
+
+# Load phenopackets
+phenopacket_dir = Path("path/to/your/fbn1_phenopackets/")
+
+phenopackets = []
+for file_path in sorted(phenopacket_dir.glob("*.json")):
+    with open(file_path, "r", encoding="utf-8") as f:
+        data: str = f.read()
+        phenopacket: Phenopacket = Parse(data, Phenopacket())
+        phenopackets.append(phenopacket)
+
+# Build dataset
+dataset = PhenotypeDatasetBuilder(phenopackets).build()
+
+# Run correlation analysis
+analyzer = HPOCorrelationAnalyzer(dataset)
+results = analyzer.compute_correlation_matrix()
+results.correlation_results.head()
+```
+
+For complete workflows, visualization options, and API details, see the [Documentation](https://phenocor.readthedocs.io/).
+
+
+

phenocor-0.2.0/README.md

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+# phenocor
+
+**phenocor** is a Python library for analyzing pairwise relationships between Human Phenotype Ontology (HPO) features in [GA4GH Phenopacket](https://www.ga4gh.org/product/phenopackets/) cohorts.
+
+It provides **Pairwise association analysis**, which measures associations between binary phenotype annotations using the phi coefficient and Fisher's exact test.
+
+
+---
+
+## Installation
+
+```bash
+pip install phenocor
+```
+
+
+## Features
+
+* Construction of phenotype matrices from GA4GH Phenopackets, with separate representation of observed, excluded, and unreported HPO annotations
+* Ontology-aware propagation of phenotype annotations
+* Pairwise phenotype association analysis using the phi coefficient, Fisher's exact test, and Benjamini–Hochberg correction, with exclusion of ancestor–descendant HPO term pairs
+* Tabular results and interactive heatmaps, including contingency counts, effective sample sizes, adjusted p-values, and publication provenance where available
+
+
+## Quickstart
+
+```python
+from pathlib import Path
+from google.protobuf.json_format import Parse
+from phenopackets import Phenopacket
+from phenocor import (
+    PhenotypeDatasetBuilder,
+    HPOCorrelationAnalyzer,
+)
+
+# Load phenopackets
+phenopacket_dir = Path("path/to/your/fbn1_phenopackets/")
+
+phenopackets = []
+for file_path in sorted(phenopacket_dir.glob("*.json")):
+    with open(file_path, "r", encoding="utf-8") as f:
+        data: str = f.read()
+        phenopacket: Phenopacket = Parse(data, Phenopacket())
+        phenopackets.append(phenopacket)
+
+# Build dataset
+dataset = PhenotypeDatasetBuilder(phenopackets).build()
+
+# Run correlation analysis
+analyzer = HPOCorrelationAnalyzer(dataset)
+results = analyzer.compute_correlation_matrix()
+results.correlation_results.head()
+```
+
+For complete workflows, visualization options, and API details, see the [Documentation](https://phenocor.readthedocs.io/).
+
+
+

phenocor-0.2.0/pyproject.toml

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+# pyproject.toml
+
+[build-system]
+requires = ["setuptools>=65.6.3", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "phenocor"
+requires-python = ">=3.10"
+description = "A Python package for correlation analysis of HPO annotations in GA4GH phenopacket cohorts"
+readme = { file = "README.md", content-type = "text/markdown" }
+authors = [
+    {name = "Jing Chen", email="jing.chen@bih-charite.de"},
+]
+maintainers =[{name = "Peter Robinson", email="peter.robinson@bih-charite.de"},
+             {name = "Daniel Danis", email="daniel.danis@bih-charite.de"},]
+license = { file = "LICENSE" }
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+]
+keywords = [
+    "Global Alliance for Genomics and Health",
+    "GA4GH Phenopacket Schema",
+    "Human Phenotype Ontology",
+    "GA4GH",
+    "HPO"]
+
+# version in __init__
+dynamic = ["version"]
+
+dependencies = [
+    "hpo-toolkit>=0.5.0,<0.6",
+    "phenopackets>=2.0.2,<3.0",
+    "scikit-learn>=1.6.1,<2.0",
+    "numpy>=1.26.4,<3.0",
+    "pandas>=2.2.3,<3.0",
+    "plotly>=6.1.1",
+    "kaleido>=1.0.0",
+    "scipy>=1.15.1,<2.0",          
+    "joblib>=1.4.2,<2.0",        
+    "tqdm>=4.67.1,<5.0",          
+    "statsmodels>=0.14.4,<1.0"
+]
+
+[project.optional-dependencies]
+test = ["pytest>=7.0.0,<8.0.0"]
+docs = [
+    'mkdocs-material[imaging]>=9.5.10,<10',
+    'mkdocs-material-extensions>=1.3,<2.0',
+    'mkdocstrings[python]>=0.22,<1.0',
+    'mkdocs-gen-files>=0.5.0',
+    'pillow',
+    'cairosvg',
+]
+
+
+
+[project.urls]
+homepage = "https://github.com/P2GX/phenocor"
+repository = "https://github.com/P2GX/phenocor.git"
+documentation = "https://P2GX.github.io/phenocor/"
+bugtracker = "https://github.com/P2GX/phenocor/issues"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+zip-safe = false
+
+[tool.setuptools.dynamic]
+version = { attr = "phenocor.__version__" }
+
+
+
+[tool.yapf]
+blank_line_before_nested_class_or_def = true
+column_limit = 88
+
+[tool.pylint]
+max-line-length = 88
+disable = [
+    "C0103", # (invalid-name)
+    "C0114", # (missing-module-docstring)
+    "C0115", # (missing-class-docstring)
+    "C0116", # (missing-function-docstring)
+    "R0903", # (too-few-public-methods)
+    "R0913", # (too-many-arguments)
+    "W0105", # (pointless-string-statement)
+]

phenocor-0.2.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

phenocor-0.2.0/src/phenocor/__init__.py

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+from .analysis import HPOCorrelationAnalyzer
+from .core import PhenotypeDatasetBuilder
+
+
+
+__version__ = "0.2.0"
+
+
+__all__ = [
+    "PhenotypeDatasetBuilder",
+    "HPOCorrelationAnalyzer",
+]

phenocor-0.2.0/src/phenocor/analysis/__init__.py

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+from .hpo_correlation_analyzer import HPOCorrelationAnalyzer
+
+__all__ = [
+    "HPOCorrelationAnalyzer",
+]