pywombat 0.1.0__tar.gz

pywombat-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:  # Allows manual trigger
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # Required for trusted publishing
+      contents: read
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build hatchling
+      
+      - name: Build package
+        run: python -m build
+      
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

pywombat-0.1.0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv
+output.tsv
+tests/*

pywombat-0.1.0/.python-version

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+3.12

pywombat-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pywombat
+Version: 0.1.0
+Summary: A CLI tool for processing and filtering bcftools tabulated TSV files with pedigree support
+Project-URL: Homepage, https://github.com/bourgeron-lab/pywombat
+Project-URL: Repository, https://github.com/bourgeron-lab/pywombat
+Project-URL: Issues, https://github.com/bourgeron-lab/pywombat/issues
+Author-email: Freddy Cliquet <fcliquet@pasteur.fr>
+License: MIT
+Keywords: bioinformatics,genomics,pedigree,variant-calling,vcf
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Requires-Dist: click>=8.1.0
+Requires-Dist: polars>=0.19.0
+Requires-Dist: pyyaml>=6.0
+Description-Content-Type: text/markdown
+
+# PyWombat
+
+A CLI tool for processing bcftools tabulated TSV files.
+
+## Installation
+
+This is a UV-managed Python package. To install:
+
+```bash
+uv sync
+```
+
+## Usage
+
+The `wombat` command processes bcftools tabulated TSV files:
+
+```bash
+# Format a bcftools TSV file and print to stdout
+wombat input.tsv
+
+# Format and save to output file (creates output.tsv by default)
+wombat input.tsv -o output
+
+# Format and save as parquet
+wombat input.tsv -o output -f parquet
+wombat input.tsv -o output --format parquet
+
+# Format with pedigree information to add parent genotypes
+wombat input.tsv --pedigree pedigree.tsv -o output
+```
+
+### What does `wombat` do?
+
+The `wombat` command processes bcftools tabulated TSV files by:
+
+1. **Expanding the `(null)` column**: This column contains multiple fields in the format `NAME=value` separated by semicolons (e.g., `DP=30;AF=0.5;AC=2`). Each field is extracted into its own column.
+
+2. **Preserving the `CSQ` column**: The CSQ (Consequence) column is preserved as-is and not melted, allowing VEP annotations to remain intact.
+
+3. **Melting and splitting sample columns**: After the `(null)` column, there are typically sample columns with values in `GT:DP:GQ:AD` format. The tool:
+   - Extracts the sample name (the part before the first `:` character)
+   - Transforms the wide format into long format
+   - Creates a `sample` column with the sample names
+   - Splits the sample values into separate columns:
+     - `sample_gt`: Genotype (e.g., 0/1, 1/1)
+     - `sample_dp`: Read depth
+     - `sample_gq`: Genotype quality
+     - `sample_ad`: Allele depth (takes the second value from comma-separated list)
+     - `sample_vaf`: Variant allele frequency (calculated as sample_ad / sample_dp)
+
+### Example
+
+**Input:**
+
+```tsv
+CHROM POS REF ALT (null) Sample1:GT:Sample1:DP:Sample1:GQ:Sample1:AD Sample2:GT:Sample2:DP:Sample2:GQ:Sample2:AD
+chr1 100 A T DP=30;AF=0.5;AC=2 0/1:15:99:5,10 1/1:18:99:0,18
+```
+
+**Output:**
+
+```tsv
+CHROM POS REF ALT AC AF DP sample sample_gt sample_dp sample_gq sample_ad sample_vaf
+chr1 100 A T 2 0.5 30 Sample1 0/1 15 99 10 0.6667
+chr1 100 A T 2 0.5 30 Sample2 1/1 18 99 18 1.0
+```
+
+Notes:
+
+- The `sample_ad` column contains the second value from the AD field (e.g., from `5,10` it extracts `10`)
+- The `sample_vaf` column is the variant allele frequency calculated as `sample_ad / sample_dp`
+- By default, output is in TSV format. Use `-f parquet` to output as Parquet files
+- The `-o` option specifies an output prefix (e.g., `-o output` creates `output.tsv` or `output.parquet`)
+
+### Pedigree Support
+
+You can provide a pedigree file with the `--pedigree` option to add parent genotype information to the output. This enables trio analysis by including the father's and mother's genotypes for each sample.
+
+**Pedigree File Format:**
+
+The pedigree file should be a tab-separated file with the following columns:
+
+- `FID`: Family ID
+- `sample_id`: Sample identifier (matches the sample names in the VCF)
+- `FatherBarcode`: Father's sample identifier (use `0` or `-9` if unknown)
+- `MotherBarcode`: Mother's sample identifier (use `0` or `-9` if unknown)
+- `Sex`: Sex of the sample (optional)
+- `Pheno`: Phenotype information (optional)
+
+Example pedigree file:
+
+```tsv
+FID sample_id FatherBarcode MotherBarcode Sex Pheno
+FAM1 Child1 Father1 Mother1 1 2
+FAM1 Father1 0 0 1 1
+FAM1 Mother1 0 0 2 1
+```
+
+**Output with Pedigree:**
+
+When using `--pedigree`, the output will include additional columns for each parent:
+
+- `father_gt`, `father_dp`, `father_gq`, `father_ad`, `father_vaf`: Father's genotype information
+- `mother_gt`, `mother_dp`, `mother_gq`, `mother_ad`, `mother_vaf`: Mother's genotype information
+
+These columns will contain the parent's genotype data for the same variant, allowing you to analyze inheritance patterns.
+
+## Development
+
+This project uses:
+
+- **UV** for package management
+- **Polars** for fast data processing
+- **Click** for CLI interface
+
+## Testing
+
+Test files are available in the `tests/` directory:
+
+- `test.tabulated.tsv` - Real bcftools output
+- `test_small.tsv` - Small example for quick testing

pywombat-0.1.0/QUICKSTART.md

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+# Wombat Quick Start
+
+## Installation
+
+```bash
+cd /Users/fcliquet/Workspace/pywombat
+uv sync
+```
+
+## Basic Usage
+
+```bash
+# Format a bcftools TSV file
+uv run wombat format tests/test.tabulated.tsv -o output.tsv
+
+# With verbose output to see progress
+uv run wombat format tests/test.tabulated.tsv -o output.tsv --verbose
+
+# Output to stdout
+uv run wombat format tests/test.tabulated.tsv
+
+# View help
+uv run wombat --help
+uv run wombat format --help
+```
+
+## What It Does
+
+### Input (Wide Format)
+
+```
+CHROM  POS  REF  ALT  (null)              Sample1:GT  Sample2:GT
+chr1   100  A    T    DP=30;AF=0.5;AC=2   0/1         1/1
+```
+
+### Output (Long Format)
+
+```
+CHROM  POS  REF  ALT  AC  AF   DP  sample   sample_value
+chr1   100  A    T    2   0.5  30  Sample1  0/1
+chr1   100  A    T    2   0.5  30  Sample2  1/1
+```
+
+## Features
+
+1. **Expands (null) column**: Splits `DP=30;AF=0.5;AC=2` into separate columns
+2. **Melts samples**: Converts wide sample columns to long format
+3. **Fast processing**: Uses Polars for efficient data handling
+
+## Testing
+
+```bash
+# Run the test suite
+uv run python tests/test_format.py
+
+# Test with small example
+uv run wombat format tests/test_small.tsv -o tests/output_small.tsv
+
+# Test with real data
+uv run wombat format tests/test.tabulated.tsv -o tests/output.tsv
+```
+
+## Project Structure
+
+```
+pywombat/
+├── pyproject.toml          # Project configuration with dependencies
+├── README.md               # Main documentation
+├── USAGE.md               # Detailed usage guide
+├── src/
+│   └── pywombat/
+│       ├── __init__.py    # Package init
+│       └── cli.py         # Main CLI implementation
+└── tests/
+    ├── test_format.py     # Unit tests
+    ├── test_small.tsv     # Small test file
+    └── test.tabulated.tsv # Real bcftools output
+```
+
+## Dependencies
+
+- **polars** (>=0.19.0): Fast DataFrame library for data processing
+- **click** (>=8.1.0): Command-line interface framework
+
+## Troubleshooting
+
+If you encounter issues:
+
+1. Make sure dependencies are installed: `uv sync`
+2. Check that input file is valid TSV with a `(null)` column
+3. Use `--verbose` flag to see processing details
+4. For large files, ensure sufficient memory is available

pywombat-0.1.0/README.md

@@ -0,0 +1,121 @@
+# PyWombat
+
+A CLI tool for processing bcftools tabulated TSV files.
+
+## Installation
+
+This is a UV-managed Python package. To install:
+
+```bash
+uv sync
+```
+
+## Usage
+
+The `wombat` command processes bcftools tabulated TSV files:
+
+```bash
+# Format a bcftools TSV file and print to stdout
+wombat input.tsv
+
+# Format and save to output file (creates output.tsv by default)
+wombat input.tsv -o output
+
+# Format and save as parquet
+wombat input.tsv -o output -f parquet
+wombat input.tsv -o output --format parquet
+
+# Format with pedigree information to add parent genotypes
+wombat input.tsv --pedigree pedigree.tsv -o output
+```
+
+### What does `wombat` do?
+
+The `wombat` command processes bcftools tabulated TSV files by:
+
+1. **Expanding the `(null)` column**: This column contains multiple fields in the format `NAME=value` separated by semicolons (e.g., `DP=30;AF=0.5;AC=2`). Each field is extracted into its own column.
+
+2. **Preserving the `CSQ` column**: The CSQ (Consequence) column is preserved as-is and not melted, allowing VEP annotations to remain intact.
+
+3. **Melting and splitting sample columns**: After the `(null)` column, there are typically sample columns with values in `GT:DP:GQ:AD` format. The tool:
+   - Extracts the sample name (the part before the first `:` character)
+   - Transforms the wide format into long format
+   - Creates a `sample` column with the sample names
+   - Splits the sample values into separate columns:
+     - `sample_gt`: Genotype (e.g., 0/1, 1/1)
+     - `sample_dp`: Read depth
+     - `sample_gq`: Genotype quality
+     - `sample_ad`: Allele depth (takes the second value from comma-separated list)
+     - `sample_vaf`: Variant allele frequency (calculated as sample_ad / sample_dp)
+
+### Example
+
+**Input:**
+
+```tsv
+CHROM POS REF ALT (null) Sample1:GT:Sample1:DP:Sample1:GQ:Sample1:AD Sample2:GT:Sample2:DP:Sample2:GQ:Sample2:AD
+chr1 100 A T DP=30;AF=0.5;AC=2 0/1:15:99:5,10 1/1:18:99:0,18
+```
+
+**Output:**
+
+```tsv
+CHROM POS REF ALT AC AF DP sample sample_gt sample_dp sample_gq sample_ad sample_vaf
+chr1 100 A T 2 0.5 30 Sample1 0/1 15 99 10 0.6667
+chr1 100 A T 2 0.5 30 Sample2 1/1 18 99 18 1.0
+```
+
+Notes:
+
+- The `sample_ad` column contains the second value from the AD field (e.g., from `5,10` it extracts `10`)
+- The `sample_vaf` column is the variant allele frequency calculated as `sample_ad / sample_dp`
+- By default, output is in TSV format. Use `-f parquet` to output as Parquet files
+- The `-o` option specifies an output prefix (e.g., `-o output` creates `output.tsv` or `output.parquet`)
+
+### Pedigree Support
+
+You can provide a pedigree file with the `--pedigree` option to add parent genotype information to the output. This enables trio analysis by including the father's and mother's genotypes for each sample.
+
+**Pedigree File Format:**
+
+The pedigree file should be a tab-separated file with the following columns:
+
+- `FID`: Family ID
+- `sample_id`: Sample identifier (matches the sample names in the VCF)
+- `FatherBarcode`: Father's sample identifier (use `0` or `-9` if unknown)
+- `MotherBarcode`: Mother's sample identifier (use `0` or `-9` if unknown)
+- `Sex`: Sex of the sample (optional)
+- `Pheno`: Phenotype information (optional)
+
+Example pedigree file:
+
+```tsv
+FID sample_id FatherBarcode MotherBarcode Sex Pheno
+FAM1 Child1 Father1 Mother1 1 2
+FAM1 Father1 0 0 1 1
+FAM1 Mother1 0 0 2 1
+```
+
+**Output with Pedigree:**
+
+When using `--pedigree`, the output will include additional columns for each parent:
+
+- `father_gt`, `father_dp`, `father_gq`, `father_ad`, `father_vaf`: Father's genotype information
+- `mother_gt`, `mother_dp`, `mother_gq`, `mother_ad`, `mother_vaf`: Mother's genotype information
+
+These columns will contain the parent's genotype data for the same variant, allowing you to analyze inheritance patterns.
+
+## Development
+
+This project uses:
+
+- **UV** for package management
+- **Polars** for fast data processing
+- **Click** for CLI interface
+
+## Testing
+
+Test files are available in the `tests/` directory:
+
+- `test.tabulated.tsv` - Real bcftools output
+- `test_small.tsv` - Small example for quick testing

pywombat-0.1.0/pyproject.toml

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+[project]
+name = "pywombat"
+version = "0.1.0"
+description = "A CLI tool for processing and filtering bcftools tabulated TSV files with pedigree support"
+readme = "README.md"
+authors = [{ name = "Freddy Cliquet", email = "fcliquet@pasteur.fr" }]
+requires-python = ">=3.12"
+dependencies = ["polars>=0.19.0", "click>=8.1.0", "pyyaml>=6.0"]
+license = { text = "MIT" }
+keywords = ["vcf", "bioinformatics", "genomics", "pedigree", "variant-calling"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+]
+
+[project.urls]
+Homepage = "https://github.com/bourgeron-lab/pywombat"
+Repository = "https://github.com/bourgeron-lab/pywombat"
+Issues = "https://github.com/bourgeron-lab/pywombat/issues"
+
+[project.scripts]
+wombat = "pywombat.cli:cli"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

pywombat-0.1.0/src/pywombat/__init__.py

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+def main() -> None:
+    print("Hello from pywombat!")