gpsea 0.2.0__tar.gz

gpsea-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2023, The Monarch Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gpsea-0.2.0/MANIFEST.in

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+include src/gpsea/model/genome/GCF_*.tsv
+include src/gpsea/view/templates/*.html

gpsea-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: gpsea
+Version: 0.2.0
+Summary: Discover genotype-phenotype correlations with GA4GH phenopackets
+Author-email: Lauren Rekerle <lauren.rekerle@jax.org>, Daniel Danis <daniel.danis@jax.org>, Peter Robinson <peter.robinson@jax.org>
+License: MIT License
+        
+        Copyright (c) 2023, The Monarch Initiative
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Project-URL: homepage, https://github.com/monarch-initiative/gpsea
+Project-URL: repository, https://github.com/monarch-initiative/gpsea.git
+Project-URL: documentation, https://monarch-initiative.github.io/gpsea/stable
+Project-URL: bugtracker, https://github.com/monarch-initiative/gpsea/issues
+Keywords: Global Alliance for Genomics and Health,GA4GH Phenopacket Schema,Human Phenotype Ontology,GA4GH,Genotype-phenotype correlation,HPO
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: hpo-toolkit>=0.3.0
+Requires-Dist: Jinja2<4.0.0,>=3.1.4
+Requires-Dist: protobuf>=3.15.0
+Requires-Dist: pandas<3.0.0,>=2.0.0
+Requires-Dist: phenopacket-store-toolkit>=0.1.2
+Requires-Dist: requests<3.0,>=2.25.0
+Requires-Dist: scipy<2.0,>=1.10
+Requires-Dist: statsmodels>=0.13.0
+Requires-Dist: numpy>=1.23
+Requires-Dist: matplotlib<4.0,>=3.2.0
+Requires-Dist: ratelimit<3,>=2.2.1
+Requires-Dist: tqdm>=4.60
+Provides-Extra: test
+Requires-Dist: pytest<8.0.0,>=7.0.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.3.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
+
+[![Build status](https://github.com/monarch-initiative/gpsea/workflows/CI/badge.svg)](https://github.com/monarch-initiative/gpsea/actions/workflows/python_ci.yml)
+[![GitHub release](https://img.shields.io/github/release/monarch-initiative/gpsea.svg)](https://github.com/monarch-initiative/gpsea/releases)
+![PyPi downloads](https://img.shields.io/pypi/dm/gpsea.svg?label=Pypi%20downloads)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/gpsea)
+
+GPSEA is a Python library for discovery of genotype-phenotype associations.
+
+An example of simple genotype-phenotype association analysis
+
+```python
+# Load HPO
+import hpotk
+
+store = hpotk.configure_ontology_store()
+hpo = store.load_minimal_hpo()
+
+# Load a cohort of phenopackets
+from gpsea.data import get_toy_cohort
+
+cohort = get_toy_cohort()
+
+# Analyze genotype-phenotype associations
+from gpsea.analysis import configure_cohort_analysis
+from gpsea.analysis.predicate import PatientCategories
+
+from gpsea.model import VariantEffect
+
+cohort_analysis = configure_cohort_analysis(cohort, hpo)
+frameshift = cohort_analysis.compare_by_variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id='NM_1234.5')
+
+frameshift.summarize(hpo, category=PatientCategories.YES)
+```
+
+provides a pandas data frame with genotype-phenotype correlations:
+
+```text
+FRAMESHIFT_VARIANT on NM_1234.5                                    No                Yes
+                                                                Count   Percent    Count   Percent    p value    Corrected p value
+    Arachnodactyly [HP:0001166]                                  1/10       10%    13/16       81%   0.000781             0.020299
+    Abnormality of the musculature [HP:0003011]                   6/6      100%    11/11      100%   1.000000             1.000000
+    Abnormal nervous system physiology [HP:0012638]               9/9      100%    15/15      100%   1.000000             1.000000
+    ...                                                           ...       ...      ...       ...        ...                  ...
+```
+
+## Documentation
+
+Check out the User guide and the API reference for more info:
+
+- [Stable documentation](https://monarch-initiative.github.io/gpsea/stable/) (last release on `main` branch)
+- [Latest documentation](https://monarch-initiative.github.io/gpsea/latest) (bleeding edge, latest commit on `develop` branch)

gpsea-0.2.0/README.md

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+[![Build status](https://github.com/monarch-initiative/gpsea/workflows/CI/badge.svg)](https://github.com/monarch-initiative/gpsea/actions/workflows/python_ci.yml)
+[![GitHub release](https://img.shields.io/github/release/monarch-initiative/gpsea.svg)](https://github.com/monarch-initiative/gpsea/releases)
+![PyPi downloads](https://img.shields.io/pypi/dm/gpsea.svg?label=Pypi%20downloads)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/gpsea)
+
+GPSEA is a Python library for discovery of genotype-phenotype associations.
+
+An example of simple genotype-phenotype association analysis
+
+```python
+# Load HPO
+import hpotk
+
+store = hpotk.configure_ontology_store()
+hpo = store.load_minimal_hpo()
+
+# Load a cohort of phenopackets
+from gpsea.data import get_toy_cohort
+
+cohort = get_toy_cohort()
+
+# Analyze genotype-phenotype associations
+from gpsea.analysis import configure_cohort_analysis
+from gpsea.analysis.predicate import PatientCategories
+
+from gpsea.model import VariantEffect
+
+cohort_analysis = configure_cohort_analysis(cohort, hpo)
+frameshift = cohort_analysis.compare_by_variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id='NM_1234.5')
+
+frameshift.summarize(hpo, category=PatientCategories.YES)
+```
+
+provides a pandas data frame with genotype-phenotype correlations:
+
+```text
+FRAMESHIFT_VARIANT on NM_1234.5                                    No                Yes
+                                                                Count   Percent    Count   Percent    p value    Corrected p value
+    Arachnodactyly [HP:0001166]                                  1/10       10%    13/16       81%   0.000781             0.020299
+    Abnormality of the musculature [HP:0003011]                   6/6      100%    11/11      100%   1.000000             1.000000
+    Abnormal nervous system physiology [HP:0012638]               9/9      100%    15/15      100%   1.000000             1.000000
+    ...                                                           ...       ...      ...       ...        ...                  ...
+```
+
+## Documentation
+
+Check out the User guide and the API reference for more info:
+
+- [Stable documentation](https://monarch-initiative.github.io/gpsea/stable/) (last release on `main` branch)
+- [Latest documentation](https://monarch-initiative.github.io/gpsea/latest) (bleeding edge, latest commit on `develop` branch)

gpsea-0.2.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gpsea"
+authors = [
+    {name = "Lauren Rekerle", email="lauren.rekerle@jax.org"},
+    {name = "Daniel Danis", email="daniel.danis@jax.org"},
+    {name = "Peter Robinson", email="peter.robinson@jax.org"},
+     ]
+description = "Discover genotype-phenotype correlations with GA4GH phenopackets"
+readme = "README.md"
+requires-python = ">=3.10"
+keywords = [
+    "Global Alliance for Genomics and Health",
+    "GA4GH Phenopacket Schema",
+    "Human Phenotype Ontology",
+    "GA4GH",
+    "Genotype-phenotype correlation",
+    "HPO",
+]
+license = { file = "LICENSE" }
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+dependencies = [
+    "hpo-toolkit>=0.3.0",
+    "Jinja2>=3.1.4,<4.0.0",
+    "protobuf>=3.15.0",
+    "pandas>=2.0.0,<3.0.0",
+    "phenopacket-store-toolkit>=0.1.2",
+    "requests>=2.25.0,<3.0",
+    "scipy>=1.10,<2.0",
+    "statsmodels>=0.13.0",
+    "numpy>=1.23",
+    "matplotlib>=3.2.0,<4.0",
+    "ratelimit>=2.2.1,<3",
+    "tqdm>=4.60",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=7.0.0,<8.0.0",
+    "pytest-cov",
+]
+docs = ["sphinx>=7.0.0", "sphinx-rtd-theme>=1.3.0", "sphinx-copybutton>=0.5.0"]
+
+[project.urls]
+homepage = "https://github.com/monarch-initiative/gpsea"
+repository = "https://github.com/monarch-initiative/gpsea.git"
+documentation = "https://monarch-initiative.github.io/gpsea/stable"
+bugtracker = "https://github.com/monarch-initiative/gpsea/issues"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.setuptools.dynamic]
+version = { attr = "gpsea.__version__" }

gpsea-0.2.0/setup.cfg

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

gpsea-0.2.0/src/gpsea/__init__.py

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+"""
+GPSEA is a library for analyzing genotype-phenotype correlations in cohorts of rare disease patients.
+"""
+
+__version__ = "0.2.0"

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

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+from ._api import CohortAnalysis, GenotypePhenotypeAnalysisResult, HpoMtcReport
+# TODO This should go away
+from ._config import CohortAnalysisConfiguration, configure_cohort_analysis, configure_default_protein_metadata_service, MtcStrategy
+from ._gp_analysis import apply_predicates_on_patients
+from ._util import prepare_hpo_terms_of_interest
+
+__all__ = [
+    'configure_cohort_analysis',
+    'CohortAnalysis', 'GenotypePhenotypeAnalysisResult',
+    'CohortAnalysisConfiguration', 'MtcStrategy',
+    'HpoMtcReport',
+    'apply_predicates_on_patients',
+    'configure_default_protein_metadata_service',
+    'prepare_hpo_terms_of_interest',
+]