voihla 0.1.0__tar.gz

voihla-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Alyssa Paynter
+
+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.

voihla-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: voihla
+Version: 0.1.0
+Summary: HLA Imputation Validation Package
+Author: Alyssa Paynter
+Author-email: Alyssa Paynter <apaynter@tulane.edu>
+License-Expression: MIT
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: scikit-learn>=1.0.0
+Requires-Dist: matplotlib>=3.3.0
+Requires-Dist: requests>=2.25.0
+Requires-Dist: py-ard>=1.0.0
+Dynamic: author
+Dynamic: license-file
+Dynamic: requires-python
+
+# VOIHLA - Validation of Imputed HLA
+
+Compute high resolution HLA imputation validation metrics using the `voihla` Python package and scikit-learn model evaluation statistics.
+
+## Overview
+
+The `voihla` package provides tools to preprocess, analyze, and visualize HLA imputation results. It supports single-locus, multilocus, and eplet-level analyses using standard metrics and calibration plots.
+
+## Installation
+
+Clone the Github repository and navigate to the project directory:
+``` bash
+git clone git@github.com:lgragert/imputation-validation.git
+```
+
+Install dependencies using pip:
+```bash
+pip install .
+```
+
+## Example Input Files
+
+- `imputation.csv`: Imputation output with predicted HLA haplotype pairs and probabilities.
+- `truth_table.csv`: High resolution genotype truth table in GLString format.
+
+Example contents of files that are input for the package:
+
+imputation.csv
+```
+ID,Rank,Hap1,Hap2,HapPair_Prob
+D3505,1,A*30:02~B*14:02,A*32:01~B*39:10,0.3150459288416418
+D3505,2,A*30:02~B*14:02,A*32:01~B*39:01,0.2673517305598033
+D3505,3,A*30:02~B*39:10,A*32:01~B*14:02,0.09971243338882652
+D3505,4,A*30:02~B*14:02,A*32:01~B*39:06,0.09552497014201682
+D3505,5,A*30:01~B*14:02,A*32:01~B*39:10,0.0787155933156964
+D3505,6,A*30:01~B*14:02,A*32:01~B*39:01,0.06679899077690125
+D3505,7,A*30:01~B*39:10,A*32:01~B*14:02,0.02920649369703246
+D3505,8,A*30:01~B*14:02,A*32:01~B*39:06,0.02386732857916924
+D3505,9,A*30:02~B*14:02,A*32:01~B*39:24,0.009453181190469357
+D3505,10,A*30:01~B*14:02,A*32:01~B*39:24,0.002361918368107546
+D3505,11,A*30:02~B*39:01,A*32:01~B*14:02,0.002257484294942207
+D13880,1,A*30:02~B*07:02,A*34:02~B*53:01,0.40269177048888066
+D13880,2,A*30:01~B*07:02,A*34:02~B*53:01,0.20308144129546576
+D13880,3,A*30:02~B*53:01,A*34:02~B*07:02,0.13918038201193
+D13880,4,A*30:01~B*53:01,A*34:02~B*07:02,0.11366198792610206
+D13880,5,A*30:02~B*07:05,A*34:02~B*53:01,0.04839353857099623
+D13880,6,A*30:01~B*07:05,A*34:02~B*53:01,0.04136109507629823
+D13880,7,A*30:02~B*53:01,A*34:02~B*07:09,0.011395011799743957
+D13880,8,A*30:02~B*53:01,A*34:02~B*07:05,0.010829180412477053
+D13880,9,A*30:01~B*53:01,A*34:02~B*07:09,0.009305763318635456
+D13880,10,A*30:01~B*53:01,A*34:02~B*07:05,0.008843675778868338
+D13880,11,A*30:04~B*53:01,A*34:02~B*07:02,0.0027297420425591353
+```
+
+`truth_table.csv`
+```
+ID,GLString
+D3505,A*30:02+A*32:01^B*14:02+B*39:01
+D13880,A*30:02+A*34:02+B*07:05+B*53:01
+```
+
+## Usage
+
+All main modules are in the `voihla` folder.
+
+### Preprocessing
+
+Convert raw imputation files to analysis-ready format:
+
+```python
+from voihla.preprocessing import ImputationPreprocessor
+
+preprocessor = ImputationPreprocessor()
+top_impute = preprocessor.process_files(['imputation.csv']) # Can pass multiple files in a list
+top_impute.to_csv('lowres_topprob_impute.csv', index=False)
+```
+
+This will create a variable that will have every GLString in the imputation file ready for SLUG and MUG analyses depending on how many loci are avaialble in your file.
+
+### Single-Locus Analysis
+```Python
+import pandas as pd
+from voihla.analysis import SingleLocusAnalysis
+from voihla.preprocessing import ImputationPreprocessor
+
+preprocessor = ImputationPreprocessor()
+impute_df = preprocessor.process_files(['imputation.csv'])
+truth_df = pd.read_csv('truth_table.csv')  # If your truth table is in a clean format then you just need to create a DataFrame
+analysis = SingleLocusAnalysis(truth_df, impute_df)
+results = analysis.get_results_df()
+print(results)
+```
+
+The `results` DataFrame will contain the the variables required for Calibration plots.
+
+y_true = if the imputation matches the truth table then 1, otherwise 0.
+
+y_pred = the confidence of the imputation prediction being correct 1, otherwise 0 (threshold is 0.5 and can be changed).
+
+y_prob = the actual probability of the imputation.
+
+### Multilocus Analysis
+```Python
+from voihla import ImputationPreprocessor, MultiLocusAnalysis
+import pandas as pd
+
+preprocessor = ImputationPreprocessor()
+impute_df = preprocessor.process_files(['imputation.csv'])
+truth_df = pd.read_csv('truth_table.csv') 
+analysis = MultiLocusAnalysis(truth_df, impute_df)
+results = analysis.get_results_df()
+print(results)
+```
+The `results` DataFrame will contain the the variables required for Calibration plots.
+
+y_true = if the imputation matches the truth table then 1, otherwise 0.
+
+y_pred = the confidence of the imputation prediction being correct 1, otherwise 0 (threshold is 0.5 and can be changed).
+
+y_prob = the actual probability of the imputation.
+
+
+### Calibration Plots
+
+Calibration plots can be generated using the `CalibrationPlotter` class from the `voihla.plotting` module.
+
+Can take either SingleLocusAnalysis or MultiLocusAnalysis results DataFrame as input.
+
+``` Python
+from voihla.plotting import CalibrationPlotter
+
+plotter = CalibrationPlotter(n_bins=4)
+locus = 'A'
+df = analysis.get_results_df()[locus]
+fig = plotter.calibration_plot(analysis_results=df, title=f'Calibration {locus}', save_path=f'Calibration_{locus}.png')
+```
+
+### Eplet-Level Analysis
+Still a work in progress, but you can use the following code to get simulated pairs for now.
+```python
+from voihla.eplet import MonteCarloEpletAnalysis
+
+eplet_analysis = MonteCarloEpletAnalysis(api_key='YOUR_API_KEY')
+pairs_df = eplet_analysis.create_random_pairs('truth_table.csv', n_pairs=100)
+results_df = eplet_analysis.analyze_eplet_mismatches(pairs_df)
+results_df.to_csv('DRDQ_eplet_lowres_impute100.csv', index=False)
+```
+
+### Output
+- Calibration plots saved as PNG files
+- ROC curves saved as PNG files
+- Classification reports
+- Summary CSV files
+
+### API Reference
+Please go to the Eplet Registry for an API key.
+

voihla-0.1.0/README.md

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+# VOIHLA - Validation of Imputed HLA
+
+Compute high resolution HLA imputation validation metrics using the `voihla` Python package and scikit-learn model evaluation statistics.
+
+## Overview
+
+The `voihla` package provides tools to preprocess, analyze, and visualize HLA imputation results. It supports single-locus, multilocus, and eplet-level analyses using standard metrics and calibration plots.
+
+## Installation
+
+Clone the Github repository and navigate to the project directory:
+``` bash
+git clone git@github.com:lgragert/imputation-validation.git
+```
+
+Install dependencies using pip:
+```bash
+pip install .
+```
+
+## Example Input Files
+
+- `imputation.csv`: Imputation output with predicted HLA haplotype pairs and probabilities.
+- `truth_table.csv`: High resolution genotype truth table in GLString format.
+
+Example contents of files that are input for the package:
+
+imputation.csv
+```
+ID,Rank,Hap1,Hap2,HapPair_Prob
+D3505,1,A*30:02~B*14:02,A*32:01~B*39:10,0.3150459288416418
+D3505,2,A*30:02~B*14:02,A*32:01~B*39:01,0.2673517305598033
+D3505,3,A*30:02~B*39:10,A*32:01~B*14:02,0.09971243338882652
+D3505,4,A*30:02~B*14:02,A*32:01~B*39:06,0.09552497014201682
+D3505,5,A*30:01~B*14:02,A*32:01~B*39:10,0.0787155933156964
+D3505,6,A*30:01~B*14:02,A*32:01~B*39:01,0.06679899077690125
+D3505,7,A*30:01~B*39:10,A*32:01~B*14:02,0.02920649369703246
+D3505,8,A*30:01~B*14:02,A*32:01~B*39:06,0.02386732857916924
+D3505,9,A*30:02~B*14:02,A*32:01~B*39:24,0.009453181190469357
+D3505,10,A*30:01~B*14:02,A*32:01~B*39:24,0.002361918368107546
+D3505,11,A*30:02~B*39:01,A*32:01~B*14:02,0.002257484294942207
+D13880,1,A*30:02~B*07:02,A*34:02~B*53:01,0.40269177048888066
+D13880,2,A*30:01~B*07:02,A*34:02~B*53:01,0.20308144129546576
+D13880,3,A*30:02~B*53:01,A*34:02~B*07:02,0.13918038201193
+D13880,4,A*30:01~B*53:01,A*34:02~B*07:02,0.11366198792610206
+D13880,5,A*30:02~B*07:05,A*34:02~B*53:01,0.04839353857099623
+D13880,6,A*30:01~B*07:05,A*34:02~B*53:01,0.04136109507629823
+D13880,7,A*30:02~B*53:01,A*34:02~B*07:09,0.011395011799743957
+D13880,8,A*30:02~B*53:01,A*34:02~B*07:05,0.010829180412477053
+D13880,9,A*30:01~B*53:01,A*34:02~B*07:09,0.009305763318635456
+D13880,10,A*30:01~B*53:01,A*34:02~B*07:05,0.008843675778868338
+D13880,11,A*30:04~B*53:01,A*34:02~B*07:02,0.0027297420425591353
+```
+
+`truth_table.csv`
+```
+ID,GLString
+D3505,A*30:02+A*32:01^B*14:02+B*39:01
+D13880,A*30:02+A*34:02+B*07:05+B*53:01
+```
+
+## Usage
+
+All main modules are in the `voihla` folder.
+
+### Preprocessing
+
+Convert raw imputation files to analysis-ready format:
+
+```python
+from voihla.preprocessing import ImputationPreprocessor
+
+preprocessor = ImputationPreprocessor()
+top_impute = preprocessor.process_files(['imputation.csv']) # Can pass multiple files in a list
+top_impute.to_csv('lowres_topprob_impute.csv', index=False)
+```
+
+This will create a variable that will have every GLString in the imputation file ready for SLUG and MUG analyses depending on how many loci are avaialble in your file.
+
+### Single-Locus Analysis
+```Python
+import pandas as pd
+from voihla.analysis import SingleLocusAnalysis
+from voihla.preprocessing import ImputationPreprocessor
+
+preprocessor = ImputationPreprocessor()
+impute_df = preprocessor.process_files(['imputation.csv'])
+truth_df = pd.read_csv('truth_table.csv')  # If your truth table is in a clean format then you just need to create a DataFrame
+analysis = SingleLocusAnalysis(truth_df, impute_df)
+results = analysis.get_results_df()
+print(results)
+```
+
+The `results` DataFrame will contain the the variables required for Calibration plots.
+
+y_true = if the imputation matches the truth table then 1, otherwise 0.
+
+y_pred = the confidence of the imputation prediction being correct 1, otherwise 0 (threshold is 0.5 and can be changed).
+
+y_prob = the actual probability of the imputation.
+
+### Multilocus Analysis
+```Python
+from voihla import ImputationPreprocessor, MultiLocusAnalysis
+import pandas as pd
+
+preprocessor = ImputationPreprocessor()
+impute_df = preprocessor.process_files(['imputation.csv'])
+truth_df = pd.read_csv('truth_table.csv') 
+analysis = MultiLocusAnalysis(truth_df, impute_df)
+results = analysis.get_results_df()
+print(results)
+```
+The `results` DataFrame will contain the the variables required for Calibration plots.
+
+y_true = if the imputation matches the truth table then 1, otherwise 0.
+
+y_pred = the confidence of the imputation prediction being correct 1, otherwise 0 (threshold is 0.5 and can be changed).
+
+y_prob = the actual probability of the imputation.
+
+
+### Calibration Plots
+
+Calibration plots can be generated using the `CalibrationPlotter` class from the `voihla.plotting` module.
+
+Can take either SingleLocusAnalysis or MultiLocusAnalysis results DataFrame as input.
+
+``` Python
+from voihla.plotting import CalibrationPlotter
+
+plotter = CalibrationPlotter(n_bins=4)
+locus = 'A'
+df = analysis.get_results_df()[locus]
+fig = plotter.calibration_plot(analysis_results=df, title=f'Calibration {locus}', save_path=f'Calibration_{locus}.png')
+```
+
+### Eplet-Level Analysis
+Still a work in progress, but you can use the following code to get simulated pairs for now.
+```python
+from voihla.eplet import MonteCarloEpletAnalysis
+
+eplet_analysis = MonteCarloEpletAnalysis(api_key='YOUR_API_KEY')
+pairs_df = eplet_analysis.create_random_pairs('truth_table.csv', n_pairs=100)
+results_df = eplet_analysis.analyze_eplet_mismatches(pairs_df)
+results_df.to_csv('DRDQ_eplet_lowres_impute100.csv', index=False)
+```
+
+### Output
+- Calibration plots saved as PNG files
+- ROC curves saved as PNG files
+- Classification reports
+- Summary CSV files
+
+### API Reference
+Please go to the Eplet Registry for an API key.
+

voihla-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "voihla"
+version = "0.1.0"
+description = "HLA Imputation Validation Package"
+authors = [{name = "Alyssa Paynter", email = "apaynter@tulane.edu"}]
+dependencies = ["pandas>=1.3.0",
+    "numpy>=1.20.0",
+    "scikit-learn>=1.0.0",
+    "matplotlib>=3.3.0",
+    "requests>=2.25.0",
+    "py-ard>=1.0.0"]
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.8"

voihla-0.1.0/setup.cfg

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

voihla-0.1.0/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name="voihla",
+    version="0.1.0",
+    author="Alyssa Paynter",
+    description="Python package for HLA imputation validation metrics using scikit-learn",
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
+    packages=find_packages(),
+    install_requires=[
+        "pandas>=1.3.0",
+        "numpy>=1.20.0",
+        "scikit-learn>=1.0.0",
+        "matplotlib>=3.3.0",
+        "requests>=2.25.0",
+        "pyard>=2.0.0"
+    ],
+    python_requires=">=3.8",
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+    ],
+)

voihla-0.1.0/voihla/__init__.py

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+"""HLA Imputation Validation Package."""
+
+__version__ = "0.1.0"
+
+from .analysis import SingleLocusAnalysis, MultiLocusAnalysis
+from .plotting import CalibrationPlotter
+from .preprocessing import ImputationPreprocessor
+from .eplet import MonteCarloEpletAnalysis, EpletAnalysis
+
+__all__ = [
+    "SingleLocusAnalysis",
+    "MultiLocusAnalysis",
+    "CalibrationPlotter",
+    "ImputationPreprocessor",
+    "MonteCarloEpletAnalysis",
+    "EpletAnalysis"
+]