pywombat 0.5.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

pywombat-0.5.0.dist-info/METADATA

@@ -1,142 +0,0 @@
-Metadata-Version: 2.4
-Name: pywombat
-Version: 0.5.0
-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-0.5.0.dist-info/RECORD

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